title: RNase III mutant + RNase III(3xFLAG), 40 minutes, biol rep 2

description:
Library name: sample 9
rnc_VC_R1_40m.bam

tag: strain


title: Patient1, MarcoLo,  Marco-IBA-Des-, 005

status: Public on May 30 2025

type: SRA

city: ROCHESTER

first: William

last: Sherman

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

country: USA

institute: Mayo Clinic

description:
Library name: L1_MarcoLo_005 | Else
FFPE GeoMx sequencing

library_source: transcriptomic

data_processing:
Sequencing data were processed following the NanoString Standard Standalone Pipeline (2.3.3.10) and Illumina's bcl2fastq (2.20.0.422) to perform the initial demultiplex.
Digital count conversion (DCC) files were processed in R (4.2.2) using GeomxTools (3.2.0) and NanoStringNCTools (1.6.1).
QC and normalization was done following NanoString guidelines for Data QC for NGS Readout.
Differential expression analysis was performed using GeomxTools (3.2.0).
Assembly: mm10
Supplementary files format and content: comma-separated files with normalized GeoMx-Seq gene expression
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Library prep was completed following the NanoString Library Prep protocol
GeoMx-Seq

treatment_protocol: ROI segmentation was automatically performed by the GeoMx DSP analysis suite software based on the morphology markers signal, and the ROIs were divided into four segments: DESMIN+ (DESMIN+/MARCO-/IBA1-), MARCO+ (DESMIN-/MARCO+/IBA1+), MARCO- (DESMIN-/MARCO-/IBA1+) and ELSE (DESMIN-/MARCO-/IBA1-). 13-14 ROIs were selected on each liver sample; 6/7 were MARCO-High, and 6/7 were MARCO-Low, with 216 segments (libraries).

tag: tissue

value: liver

tag: disease

value: fibrosis

tag: cell type

value: Other

tag: treatment

value: treated CCl4


title: RNase J mutant reproductive, 18h, biol rep 2

city: Hamilton

first: Marie

last: Elliot

state: Ontario

address: 1280 Main Street W

department: Biology

country: Canada

institute: McMaster University

description:
Library name: sample 15
rnj_18h_R2.bam

data_processing:
Reads were aligned to the Streptomyces venezuelae NRRL B-65442 genome (NCBI accession: NZ_CP018074.1) using the BowTie2 program and the aligned files were sorted using SamTools. The number of reads aligning to genomic features were counted using the HTseq-count program for each replicate. The HTseq-count tables were then normalized and used for differential transcript level analysis with the program DESeq2.
For transcriptomic analysis of the RNase mutants compared to wild type Streptomyces venezuelae these data were filtered by significance (adjusted p-value < 0.05), expression (BaseMean > 50), and differential expression (log2 fold change > |2|)
Assembly: Streptomyces venezuelae NRRL B-65442 genome (NCBI accession: NZ_CP018074.1)
Supplementary files format and content: csv fle includes normalized counts (extracted from DESeq2 analysis) for each sample

organism: Streptomyces venezuelae

source_name: bacterial cell

growth_protocol: Streptomyces venezuelae cultures were grown in MYM (1% malt extract, 0.4%yeast extract, 0.4% maltose) at 30°C. Overnight culured were diluted to 0.1 OD(600) and grown for 10-24 h at 200 RPM.

extract_protocol:
Cells were lysed by vortexing pellets for 2 min with an approximately equal volume of sterile glass beads and ice cold lysis solution (4M guanidine thiocyanate, 25 mM trisodium citrate, 0.5%v/v sodium N-lauroylsarcosinate, 0.8%v/v β-mercaptoethanol). An equal volume of phenol:chloroform:isoamyl alcohol (50:50:1, pH 4.6) was added to the lysate and samples were vortexed on and off in thirty second intervals to emulsify the solutions. Samples were then centrifuged at 7,800 ×g and the aqueous phase containing the RNA was recovered. Total RNA was precipitated by adding an equal volume of ice-cold isopropanol (100%), 0.1 volume of sodium acetate buffer (3 M, pH 6), and 2 μL of RNA grade glycogen (ThermoFisher Scientific).The total RNA sample was DNase treated post-extraction using TURBO DNase buffer and enzyme (Fisher Scientific). Total RNA was extracted from the reaction mixture with phenol:chloroform:isoamyl alcohol (50:50:1, pH=4.6).
RNA-sequencing was conducted by the MOBIX facility at McMaster University using paired-end technology on the Illumina MiSeq v3 platform.

value: bacterial cell

tag: genotype

value: RNase J mutant

tag: time


title: Patient1, MarcoLo,  Marco+IBA+, 006

description:
Library name: L1_MarcoLo_006 | Marco+IBA+
FFPE GeoMx sequencing

value: Macrophage


title: RNase J mutant vegetative, 12h, biol rep 2

description:
Library name: sample 14
rnj_12h_R2.bam


title: RNase III mutant sporulating, 20h, biol rep 2

description:
Library name: sample 13
rnc_20h_R2.bam

value: RNase III mutant


title: RNase III mutant reproductive, 14h, biol rep 2

description:
Library name: sample 12
rnc_14h_R2.bam


title: Patient1, MarcoLo,  Des+, 005

description:
Library name: L1_MarcoLo_005 | Des+
FFPE GeoMx sequencing

value: HSC


title: Patient1, MarcoLo,  Marco+IBA+, 005

description:
Library name: L1_MarcoLo_005 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient1, MarcoLo,  Marco-IBA-Des-, 004

description:
Library name: L1_MarcoLo_004 | Else
FFPE GeoMx sequencing


title: Patient1, MarcoLo,  Marco-IBA+, 005

description:
Library name: L1_MarcoLo_005 | Marco-IBA+
FFPE GeoMx sequencing


title: wild type vegetative, 10h, biol rep 2

description:
Library name: sample 9
WT_10h_R2.bam

value: wild type


title: Patient1, MarcoLo,  Marco-IBA+, 004

description:
Library name: L1_MarcoLo_004 | Marco-IBA+
FFPE GeoMx sequencing


title: Patient1, MarcoLo,  Marco+IBA+, 004

description:
Library name: L1_MarcoLo_004 | Marco+IBA+
FFPE GeoMx sequencing


title: wild type reproductive, 14h, biol rep 2

description:
Library name: sample 10
WT_14h_R2.bam


title: Patient1, MarcoLo,  Des+, 004

description:
Library name: L1_MarcoLo_004 | Des+
FFPE GeoMx sequencing


title: RNase J mutant vegetative, 12h, biol rep 1

description:
Library name: sample 6
rnj_12h_R1.bam


title: RNase J mutant sporulating, 24h, biol rep 1

description:
Library name: sample 8
rnj_24h_R1.bam


title: Patient1, MarcoLo,  Des+, 003

description:
Library name: L1_MarcoLo_003 | Des+
FFPE GeoMx sequencing


title: RNase III mutant sporulating, 20h, biol rep 1

description:
Library name: sample 5
rnc_20h_R1.bam


title: Patient1, MarcoLo,  Marco-IBA-Des-, 003

description:
Library name: L1_MarcoLo_003 | Else
FFPE GeoMx sequencing


title: RNase III mutant vegetative, 10h, biol rep 1

description:
Library name: sample 3
rnc_10h_R1.bam


title: Patient1, MarcoLo,  Des+, 002

description:
Library name: L1_MarcoLo_002 | Des+
FFPE GeoMx sequencing


title: Patient1, MarcoLo,  Marco+IBA+, 003

description:
Library name: L1_MarcoLo_003 | Marco+IBA+
FFPE GeoMx sequencing


title: RNase III mutant reproductive, 14h, biol rep 1

description:
Library name: sample 4
rnc_14h_R1.bam


title: Patient1, MarcoLo,  Marco-IBA-Des-, 002

description:
Library name: L1_MarcoLo_002 | Else
FFPE GeoMx sequencing


title: Patient1, MarcoLo,  Marco-IBA+, 002

description:
Library name: L1_MarcoLo_002 | Marco-IBA+
FFPE GeoMx sequencing


title: RNase III mutant vegetative, 10h, biol rep

description:
Library name: sample 11
rnc_10h_R2.bam


title: Patient1, MarcoLo,  Marco-IBA-Des-, 001

description:
Library name: L1_MarcoLo_001 | Else
FFPE GeoMx sequencing


title: CJ positive_2

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

data_processing:
PartekTM FlowTM software (version 11) bulk RNA-seq pipeline was used for data analysis. In summary, trimmed reads were aligned to the Rnor_6.0 (rn6) genome reference using STAR  (version 2.7.8), and subsequently Partek E/M algorithm was used to count reads mapping to the genes from Ensembl release 95. We applied DESeq2 normalization method
Assembly: Rnor_6.0 (rn6)
Supplementary files format and content: tab-delimited file includes raw counts for each sample

organism: Rattus norvegicus

source_name: brain

growth_protocol: Thawed untreated normal cells from these different passages were either allowed to proliferate, or maintained in an arrested state for the indicated days of each passage set. Low passage post-mitotic rat Septal (SEP) neurons, immortalized with a temperature sensitive ts-SV40 T antigen (subclone e422, [1]), were passaged every 4 days at 1:4 in a proliferating state at 33oC in 10% serum-DMEM. To induce and maintain arrest, cells were cultured in 2% serum-DMEM at 37.5oC and refed every 2 days without splitting

extract_protocol:
Between 72-92 ng of RNA per sample was subjected to rRNA depletion via the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat; NEB #E7400) using the manufacturer’s protocol except that a Monarch® RNA Cleanup Kit (10 µg; NEB# T2030) was used to purify the rRNA-depleted RNA
The rRNA-depleted RNA was converted into Illumina-compatible DNA libraries via the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads kit (NEB# E7765) using the manufacturer’s protocol for use with rRNA-depleted RNA and NEBNext® Multiplex Oligos for Illumina® (NEB# E6448). Samples were pooled and sequenced 2x150 nt paired-end on an Illumina® Novaseq 6000 instrument

value: brain

value: neurons

tag: cell subtype

value: postmitotic septal neurons


title: wild type vegetative, 10h, biol rep 1

description:
Library name: sample 1
WT_10h_R1.bam


title: wild type reproductive, 14h, biol rep 1

description:
Library name: sample 2
WT_14h_R1.bam


title: Patient1, MarcoLo,  Marco+IBA+, 002

description:
Library name: L1_MarcoLo_002 | Marco+IBA+
FFPE GeoMx sequencing


title: CJ negative_2


title: CJ positive_1


title: Patient1, MarcoHi,  Marco-IBA-Des-, 006

description:
Library name: L1_MarcoHi_006 | Else
FFPE GeoMx sequencing


title: RNase J mutant reproductive, 18h, biol rep 1

description:
Library name: sample 7
rnj_18h_R1.bam


title: Patient1, MarcoLo,  Marco+IBA+, 001

description:
Library name: L1_MarcoLo_001 | Marco+IBA+
FFPE GeoMx sequencing


title: CJ negative_1


title: Patient1, MarcoHi,  Des+, 006

description:
Library name: L1_MarcoHi_006 | Des+
FFPE GeoMx sequencing


title: Patient1, MarcoHi,  Marco+IBA+, 006

description:
Library name: L1_MarcoHi_006 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient1, MarcoHi,  Marco-IBA-Des-, 005

description:
Library name: L1_MarcoHi_005 | Else
FFPE GeoMx sequencing


title: Arrest Normal_3


title: Proliferating Normal_2


title: Patient1, MarcoHi,  Des+, 005

description:
Library name: L1_MarcoHi_005 | Des+
FFPE GeoMx sequencing


title: Arrest Normal_1


title: Arrest Normal_2


title: Patient1, MarcoHi,  Marco-IBA+, 005

description:
Library name: L1_MarcoHi_005 | Marco-IBA+
FFPE GeoMx sequencing


title: Proliferating Normal_1


title: Patient1, MarcoHi,  Marco-IBA-Des-, 004

description:
Library name: L1_MarcoHi_004 | Else
FFPE GeoMx sequencing


title: Patient1, MarcoHi,  Des+, 004

description:
Library name: L1_MarcoHi_004 | Des+
FFPE GeoMx sequencing


title: K562 cells, NLS_TadA-8e expression, treatment sample, gDNA-seq

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake university

description: Library name: K562 Nuc_gDNA-seq

library_source: genomic

data_processing:
For tRNA-seq library, the tRNA clusters were identified using ‘tRNAscan-SE’ v2.0.12 with the ‘-b -q’ parameters based on the human hg38 reference genome. The tRNA masked reference was generated using ‘bedtools’ v2.27.0 with ‘-mc N’ parameter. The pre-tRNA reference was generated by adding 50nt 5' and 3' flanking regions to each tRNA. The mature tRNA reference was generated by adding a CCA tail to each tRNA and pseudogenes were removed. Sequencing reads were then trimmed using ‘cutadapt’ (version 2.6) with parameters ‘-n 1 -e 0.1 -O 2 -m 2’, and mapped to the reference using a matured pipeline for tRNAs analysis (https://github.com/hexavier/tRNA_mapping). Pre-alignment was conducted using ‘segemehl’ v2.0.12 with ‘--silent --evalue 500 --differences 3 --maxinterval 1000 --accuracy 80’ parameters, against the tRNA masked and pre-tRNA reference. Reads mapped to the masked genome and pre-tRNAs were removed. The remaining reads were re-aligned to the mature tRNA reference using ‘segemehl’ v2.0.12 with ‘--silent --evalue 500 --differences 3 --maxinterval 1000 --accuracy 85’ parameters. The aligned reads were filtered by mapping quality lower than 60, and only those with ‘NH:i:1’ flag were retained. The ‘REDItools2’ v2.0 was used to calculate the mutation sites in each sample, and the parameters were set as ‘-q 25 -bq 20 -s 0’. A custom Perl script was used to quantify the A-to-I editing events. Reads with quality lower than 25, base quality lower than 20, reads coverage lower than 10, sites annotated in dbSNP database, and A-to-I events lower than 2 were excluded. The mutated and non-mutated read counts were treated as a contingency table, and the significance of the differences was evaluated using Fisher's exact test. The p-value was adjusted using the Benjamini-Hochberg (BH) correction method.
For gDNA-seq library, sequencing reads were trimmed using ‘cutadapt’ v2.6 with ‘-n 1 -e 0.1 -O 2 -m 16’ parameters. Alignment was conducted using STAR with ‘--outFilterMultimapNmax 20 --alignEndsType EndToEnd --outReadsUnmapped Fastx 2 –outSAMstrandField intronMotif --outFilterMismatchNmax 20’, against the human hg38 genome. The aligned reads were filtered using ‘SAMtools’ with ‘-F 3332 -f 2’, and only those with ‘NH:i:1’ flag were retained. PCR duplicates were removed using ‘MarkDuplicates’ v2.22.8 from Picard with default settings. The ‘REDItools2’ v2.0 was used to calculate the mutation sites in each sample, and the parameters were set as ‘-q 25 -bq 20 -s 0’. A-to-G modification site was identified and selected as the tRNA-seq library.
Assembly: human hg38 reference
Supplementary files format and content: Tab-delimited text files include count and modification rate of A2G for A/T sites of human hg38 reference genome.

molecule: genomic DNA

organism: Homo sapiens

source_name: Bone marrow

growth_protocol: HEK293T cells were cultured in DMEM (high glucose) medium supplemented with 10% FBS and 1% PS at 37 °C with 5% CO2. K562 cells were cultured in 1640 medium supplemented with 10% FBS (Gibco) and 1% PS at 37 °C with 5% CO2.

extract_protocol:
GFP-positive cells were sorted via flow cytometry and lysed with RNAiso Plus (Takara). Total RNA was extracted using the RNAiso Plus protocol and treated with TurboDNase (Invitrogen) according to the manufacturer’s instructions. Genomic DNA was extracted using a commercial kit (Tiangen) following the manufacturer’s protocol.
tRNA-seq and gDNA-seq libraries were prepared using the QIAseq miRNA Library Kit (Qiagen) and TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme), respectively, in strict accordance with the manufacturers’ guidelines.

treatment_protocol: TadA-8e expression plasmids and GFP control plasmids were transfected into HEK293T cells by lipofectamine™ 3000 (Invitrogen) according to the manufacturer's instructions. TadA-8e expression plasmids and GFP control plasmids were delivered into K562 cells through an electroporation system (BTX, Gemini X2) in Opti-MEM (Gibco) medium.

value: Bone marrow

tag: cell line

value: Erythroleukemic cell

value: WT

value: NLS_TadA-8e_GFP transient expression


title: K562 cells, TadA-8e depletion, control sample, gDNA-seq

description: Library name: K562 Ctl_gDNA-seq

value: GFP transient expression


title: HEK293T cells, NES_TadA-8e expression, treatment sample, tRNA-seq

description: Library name: HEK293T Cyt_tRNA-seq

library_source: other

molecule: other

source_name: Human embryonic kidney

value: Human embryonic kidney

value: Human embryonic kidney cell,containing the SV40 T-antigen

value: NES_TadA-8e_GFP transient expression


title: Patient1, MarcoHi,  Marco-IBA-Des-, 003

description:
Library name: L1_MarcoHi_003 | Else
FFPE GeoMx sequencing

value: liver

value: fibrosis

value: Other

value: treated CCl4


title: HEK293T cells, NLS_TadA-8e expression, treatment sample, tRNA-seq

description: Library name: HEK293T Nuc_tRNA-seq


title: Patient1, MarcoHi,  Marco+IBA+, 003

description:
Library name: L1_MarcoHi_003 | Marco+IBA+
FFPE GeoMx sequencing

value: Macrophage


title: Patient1, MarcoHi,  Des+, 003

description:
Library name: L1_MarcoHi_003 | Des+
FFPE GeoMx sequencing

value: HSC


title: HEK293T cells, TadA-8e depletion, control sample, tRNA-seq

description: Library name: HEK293T Ctl_tRNA-seq


title: HEK293T cells, NES_TadA-8e expression, Smart-seq2, single cell 10

description: HEK293 Cyt_scTAS-seq_10

library_source: transcriptomic single cell

data_processing:
The sequencing reads were firstly undergone adapter removal by ‘cutadapt’. The parameters were set as ‘-n 1 -e 0.1 -O 2 -m 16’.
For poly(A) RNA and total RNA (ribo-minus) libraries, alignment was conducted using STAR with '--outFilterMultimapNmax 20 --alignEndsType EndToEnd --outReadsUnmapped Fastx 2 –outSAMstrandField intronMotif --outFilterMismatchNmax 20', against the human hg38 genome.
For total RNA libraries, customized references were used according to the human 45S rRNA (NR_046235.3) and snRNAs (U1: NR_004430, U2: NR_002716.3, and U4: NR_003925.1), and alignment was conducted using bowtie2 with ‘-q -k 2 -X 500 --no-discordant --no-mixed --no-unal’.
For single-cell libraries, alignment was conducted using STAR with '--outFilterMultimapNmax 20 --alignEndsType EndToEnd --outReadsUnmapped Fastx 2 --outSAMstrandField intronMotif --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterMismatchNmax 10', against the human hg38 genome.
The aligned reads were filtered by 'SAMtools' with '-F 3332 -f 2', and only those with 'NH:i:1' flag were retained. The REDItools2 was used to calculate the mutation sites in each sample, and the parameters were set as '-q 25 -S' (for single-cell data, the parameters were set as '-q 25 -bq 20 -s 0'). A custom Perl script was used to quantify the A-to-I editing events. Reads with quality lower than 25, base quality lower than 20, reads coverage lower than 10, sites annotated in dbSNP database, and A-to-I events lower than 2 were excluded.
For bulk analysis, the mutated and non-mutated read counts were treated as a contingency table, and the significance of the differences was evaluated using Fisher's exact test. The p-value was adjusted using the Benjamini-Hochberg (BH) correction method. Sites with mutation rates (treatment minus control) greater than 0 and adjusted p-value (Padj) lower than 0.05 for both replicates and located in gene body regions were retained, and their average mutation rate was considered the reliable mutation rate (RMR).
For single-cell analysis, endogenous deaminase sites in the bulk control data with a mutation rate exceeding the average were excluded from the single-cell modification sites. A-to-G mutation sites were assigned to plus-strand genes, while T-to-C mutation sites were assigned to minus-strand genes.
Assembly: hg38 or human NR_046235.3, NR_004430, NR_002716.3, and NR_003925.1 reference
Supplementary files format and content: Tab-delimited text files include reliable mutation rate of A2G for A/T sites of human hg38 reference genome.

molecule: polyA RNA

extract_protocol:
GFP-positive cells were sorted using flow cytometry and lysed with RNAiso Plus (Takara). Total RNA was then extracted and treated with TurboDNase (Invitrogen) following the manufacturer's instructions.
For the PolyA+ library, RNAs with polyA tails were selected from the total RNA using mRNA Capture Beads 2.0 (Vazyme, Cat. No. N403). For the Ribo- library, rRNAs were removed from the total RNA using the Ribo-off rRNA Depletion Kit (Vazyme, Cat. No. R406). For the Total-RNA library, total RNA was directly used for library construction. All RNA-seq libraries were constructed using the VAHTS® Stranded mRNA-seq Library Prep Kit for Illumina® V2 (Vazyme, Cat. No. NR602) according to the manufacturer's instructions. For single cells, RNA libraries were constructed using the SMART-Seq® v4 Ultra® Low Input RNA Kit (TaKaRa, Cat. No. 634891) and TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, Cat. No. TD503) according to the manufacturer’s instructions.


title: Patient1, MarcoHi,  Marco-IBA-Des-, 001

description:
Library name: L1_MarcoHi_001 | Else
FFPE GeoMx sequencing


title: Patient1, MarcoHi,  Des+, 001

description:
Library name: L1_MarcoHi_001 | Des+
FFPE GeoMx sequencing


title: Patient1, MarcoHi,  Marco+IBA+, 001

description:
Library name: L1_MarcoHi_001 | Marco+IBA+
FFPE GeoMx sequencing


title: HEK293T cells, NES_TadA-8e expression, Smart-seq2, single cell 9

description: HEK293 Cyt_scTAS-seq_9


title: HEK293T cells, NES_TadA-8e expression, Smart-seq2, single cell 8

description: HEK293 Cyt_scTAS-seq_8


title: Patient1, MarcoHi,  Marco-IBA-Des-, 0026

description:
Library name: L1_MarcoHi__0026 | Else
FFPE GeoMx sequencing


title: Patient1, MarcoHi,  Marco+IBA+, 005

description:
Library name: L1_MarcoHi_005 | Marco+IBA+
FFPE GeoMx sequencing


title: HEK293T cells, NES_TadA-8e expression, Smart-seq2, single cell 3

description: HEK293 Cyt_scTAS-seq_3


title: HEK293T cells, NES_TadA-8e expression, Smart-seq2, single cell 6

description: HEK293 Cyt_scTAS-seq_6


title: HEK293T cells, NES_TadA-8e expression, Smart-seq2, single cell 7

description: HEK293 Cyt_scTAS-seq_7


title: Patient1, MarcoHi,  Des+, 0026

description:
Library name: L1_MarcoHi__0026 | Des+
FFPE GeoMx sequencing


title: CM272 and anti-BclXL, sample 1

city: Pamplona

first: Ruben

last: Pio

state: Navarra

address: Pio XII Avenue, 55

department: Solid Tumors

country: Spain

institute: Cima Universidad de Navarra

description:
Library name: CM_BclX_1
10x Genomics

data_processing:
Cell Ranger (v7.0.0, 10x Genomics Inc) was used to align reads to the mouse genome (GRCm39) and generate gene-by-cell UMI count matrices. scRNA-seq computational guidelines were followed using R packages. Empty droplets were removed using DropleUtils 1.18.1 (FDR < 0.001). For quality control analysis, genes were filtered using SingleCellExperiment 1.20.1 based on the distribution of UMI reads, distribution of unique genes or >5% of UMIs mapped to mitochondrial genes. scDblFinder was used to identify and remove potential doublets. Genes with zero UMIs in all the cells were excluded from the analysis.
Assembly: GRCm39
Supplementary files format and content: Output files of 10x Cell Ranger software: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: LLC tumor

growth_protocol: LLC cells (2 million) were injected subcutaneously into the flanks of 8-12 week old female C57BL/6J mice.

extract_protocol:
On day 15, tumors were harvested and processed under sterile conditions. Single-cell suspensions of tumors were obtained by mechanical and enzymatic dissociation using 1 mg/mL collagenase D and 50 µg/mL DNase I at 37°C for 30 minutes. EDTA (6 µM) was then used to block collagenase and DNase I activities. Erythrocytes were lysed, and cells were resuspended in 35% Percoll solution and centrifuged at 2,000 rpm for 15 minutes without brake. The supernatant was discarded and cells were preincubated with Fc block for 15 minutes at 4ºC, and then labeled with fluorochrome-conjugated antibodies against CD45, CD11b and Ly6G. Dead cells were labeled with SYTOX Blue. CD45+ and double CD11b-/Ly6G- cells were sorted.
The transcriptome of the cells was sequenced using Single Cell 3' Reagent Kits v3.1 (10X Genomics). Briefly, 20,000 cells (except for sample Triple_2, where only 5,840 cells could be obtained) were loaded at a concentration of 1,000 cells/µL on a Chromium X instrument (10X Genomics) to capture single cells in gel bead-in-emulsions (GEMs). In this step, each cell was encapsulated with primers containing a fixed Illumina Read 1 sequence, a cell-identifying 16 nt 10X barcode, a 12 nt unique molecular identifier (UMI), and a poly-dT sequence. After cell lysis, reverse transcription yielded full-length barcoded cDNA. This cDNA was then released from the GEMs, amplified by PCR and purified using magnetic beads (SPRIselect, Beckman Coulter). Enzymatic fragmentation and size selection were used to optimize cDNA size prior to library construction. Fragmented cDNA was end-repaired, A-tailed and ligated to Illumina adaptors. A final PCR amplification with barcoded primers allowed for sample indexing. Library quality control and quantification were performed using the Qubit 3.0 Fluorometer (Life Technologies) and the 4200 TapeStation System (Agilent), respectively. Sequencing was performed on NextSeq2000 and NovaSeq6000 instruments (Illumina) aiming for at least 20,000 reads/cell.

treatment_protocol: Tumor-bearing mice were treated with vehicle, 5 mg/kg CM272 (i.p.; 5 days per week, starting on day 6), 100 μg anti-PD-1 (i.p.; days 7, 10 and 14) and/or 5 mg/kg A1331852 (i.p.; 3 days per week starting on day 7).

value: LLC tumor

value: Immune cells

value: CM272 and anti-Bcl-XL

tag: batch


title: HEK293T cells, NES_TadA-8e expression, Smart-seq2, single cell 4

description: HEK293 Cyt_scTAS-seq_4


title: anti-BclXL and anti-PD-1, sample 3

description:
Library name: BclX_aPDI_3
10x Genomics

value: anti-Bcl-XL and anti-PD-1


title: HEK293T cells, NES_TadA-8e expression, Smart-seq2, single cell 2

description: HEK293 Cyt_scTAS-seq_2


title: CM272, anti-BclXL and anti-PD-1, sample 3

description:
Library name: Triple_3
10x Genomics

value: CM272, anti-BclXL and anti-PD-1


title: HEK293T cells, NES_TadA-8e expression, Smart-seq2, single cell 5

description: HEK293 Cyt_scTAS-seq_5

value: WT


title: HEK293T cells, NES_TadA-8e expression, Smart-seq2, single cell 1

description: HEK293 Cyt_scTAS-seq_1


title: HEK293T cells, ERM_TadA-8e expression, treatment sample, tRNA-seq

description: Library name: HEK293T Erm_tRNA-seq

value: ERM_TadA-8e_GFP transient expression


title: anti-BclXL and anti-PD-1, sample 2

description:
Library name: BclX_aPDI_2
10x Genomics


title: K562 cells, NLS_TadA-8e expression, treatment sample, poly(A) RNA-seq, replicate2

description: K562 Nuc_TAS-seq replicate 2(PolyA+)

value: Bone marrow

value: Erythroleukemic cell

value: NLS_TadA-8e_GFP transient expression


title: K562 cells, NLS_TadA-8e expression, treatment sample, poly(A) RNA-seq, replicate1

description: K562 Nuc_TAS-seq replicate 1(PolyA+)


title: vehicle, sample 3

description:
Library name: Ctrl_3
10x Genomics

value: Vehicle


title: K562 cells, NES_TadA-8e expression, treatment sample, poly(A) RNA-seq, replicate2

description: K562 Cyt_TAS-seq replicate 2(PolyA+)

value: NES_TadA-8e_GFP transient expression


title: Heart, diaphragm (CkmCRE), soleus and tibialis (CkmCRE and CkmCRE; Mapk14fl/fl), scRNAseq

first: Andrés

last: Hidalgo

address: 10 Amistad Street

description: BD Rhapsody

data_processing:
Rhapsody processing pipeline
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart, diaphragm, soleus and tibialis muscles

extract_protocol:
Tissues were minced and incubated in digestion buffer for 30min at 37°C. After digestion, single-cell suspensions were obtained by gentle pipetting and mechanical dissociation of the remaining pieces through cell strainers (BD Falcon). Single-cell suspensions were incubated with conjugated antibodies against CD45 (clone 30-F11), CD45.1 (clone A20), CD45.2 (clone 104), CD11b (clone M1/70), CD64 (clone X54-5/7.1), F4/80 (clone BM8), MHCII (clone M5/114.15.2), Ly6C (clone HK1.4), ITGA7, MEFSK4 for 15 min at 4°C. For cell sorting, we used a BD FACSAria II (BDBiosciences) or BD FACSAria Fusion (BD Biosciences) cell sorters.
Library was performed according to manufacturer's instructions.

value: Leukocytes, endothelial and stromal cells

value: CkmCRE and CkmCRE; Mapk14fl/fl


title: K562 cells, NES_TadA-8e expression, treatment sample, poly(A) RNA-seq, replicate1

description: K562 Cyt_TAS-seq replicate 1(PolyA+)


title: Patient1, MarcoHi, Marco+IBA+, 0026

description:
Library name: L1_MarcoHi__0026 | Marco+IBA+
FFPE GeoMx sequencing

value: liver

value: fibrosis

value: treated CCl4


title: Pmel-1 T cells, DCA-treated, Day 7, mouse 2, H3K9Lac

city: Pittsburgh

first: Aaron

last: Yang

state: PA

address: 4401 Penn Ave

institute: University of Pittsburgh

data_processing:
trimmed high quality reads were aligned to genome  using bowtie2
bedgraph files were generated from alignment files using bedtools
BigWig files were generaed using bedGraphToBigWig
peaks were determined using MACS2 for peak calling, followed by idr
Differential peak analysis determined using DESeq2 on concatenated and merged  peak files with cutoffs of 2 fold and p value<0.05
Assembly: mm10_ensembl
Supplementary files format and content: BigWig

source_name: splenocytes

growth_protocol: To expand Pmel-1 mouse CD8+ T cells in vitro, bulk splenocytes were plated in the presence of the T cells’ cognate peptide (1uM gp100) at a concentration of 1e7 cells/mL in RPMI supplemented with 10% FBS (v/v) and 50ug/mL mouse rIL-2 at 37°C with 5% CO2 for 24 hours. After 24 hours, cells were washed with fresh RPMI and plated at a concentration of 1e6/mL with 50ug/mL IL-2. Cultures were fed daily and kept at this concentration for the duration of expansion.

extract_protocol: Libraries were amplified within CUT&Tag protocol as described (Kaya-Okur et al., 2020).  Cluster generation and 75-bp paired-end, dual-indexed sequencing were performed on the Illumina NextSeq 500 system.

treatment_protocol: 5mM DCA was added to DCA-conditioned cultures daily

value: splenocytes

tag: chip antibody

value: H3K9Lac (PTM Bio)

value: CD8+ T cell

value: B6.Cg-Thy1a/Cy Tg(TcraTcrb)8Rest/J

value: dichloroacetate (DCA)

value: Day 7


title: K562 cells, TadA-8e depletion, control sample, poly(A) RNA-seq, replicate2

description: K562 Ctl_TAS-seq replicate 2(PolyA+)

value: WT

value: GFP transient expression


title: Pmel-1 T cells, untreated, Day 7,  mouse 3, H3K9Lac

value: untreated


title: Pmel-1 T cells, untreated, Day 7, mouse 2, H3K9Lac


title: K562 cells, TadA-8e depletion, control sample, poly(A) RNA-seq, replicate1

description: K562 Ctl_TAS-seq replicate 1(PolyA+)

value: Bone marrow

value: Erythroleukemic cell


title: HEK293T cells, NLS_TadA-8e expression, treatment sample, total RNA-seq, replicate2

description: HEK293 Nuc_TAS-seq replicate 2 (Total RNA)

value: Human embryonic kidney

value: Human embryonic kidney cell,containing the SV40 T-antigen

value: NLS_TadA-8e_GFP transient expression


title: Pmel-1 T cells, DCA-treated, Day 7, mouse 3, H3K9Ac

value: H3K9Ac (Abcam)


title: HEK293T cells, NLS_TadA-8e expression, treatment sample, total RNA-seq, replicate1

description: HEK293 Nuc_TAS-seq replicate 1(Total RNA)


title: HEK293T cells, NES_TadA-8e expression, treatment sample, total RNA-seq, replicate2

description: HEK293 Cyt_TAS-seq replicate 2(Total RNA)

value: NES_TadA-8e_GFP transient expression


title: CM272 and anti-PD-1, sample 2

description:
Library name: CM_aPDI_2
10x Genomics

value: LLC tumor

value: Immune cells

value: CM272 and anti-PD-1


title: Pmel-1 T cells, DCA-treated, Day 7, mouse 3, H3K9Lac

value: splenocytes

value: H3K9Lac (PTM Bio)

value: CD8+ T cell


title: HEK293T cells, NLS_TadA-8e expression, treatment sample, total RNA-seq(rRNA depleted), replicate2

description: HEK293 Nuc_TAS-seq replicate 2 (Ribo-)


title: Pmel-1 T cells, untreated, Day 7, mouse 3, H3K9Ac

value: B6.Cg-Thy1a/Cy Tg(TcraTcrb)8Rest/J

value: Day 7


title: Pmel-1 T cells, DCA-treated, Day 7, mouse 1, H3K9Ac

value: dichloroacetate (DCA)


title: Pmel-1 T cells, untreated, Day 7, mouse 1, H3K9Ac

value: untreated


title: Pmel-1 T cells, DCA-treated, Day 7, mouse 2, H3K9Ac


title: HEK293T cells, TadA-8e depletion, control sample, total RNA-seq, replicate2

description: HEK293 Ctl_TAS-seq replicate 2(Total RNA)

value: WT

value: GFP transient expression


title: HEK293T cells, NLS_TadA-8e expression, treatment sample, total RNA-seq(rRNA depleted), replicate1

description: HEK293 Nuc_TAS-seq replicate 1(Ribo-)

value: Human embryonic kidney


title: Pmel-1 T cells, DCA-treated, Day 7, mouse 2, H3K27Ac

value: H3K27Ac (Abcam)


title: HEK293T cells, TadA-8e depletion, control sample, total RNA-seq, replicate1

description: HEK293 Ctl_TAS-seq replicate 1(Total RNA)

value: Human embryonic kidney cell,containing the SV40 T-antigen


title: Pmel-1 T cells, untreated, Day 7, mouse 2, H3K9Ac

value: H3K9Ac (Abcam)


title: Pmel-1 T cells, DCA-treated, Day 7, mouse 3, H3K27Ac


title: HEK293T cells, NES_TadA-8e expression, treatment sample, total RNA-seq(rRNA depleted), replicate2

description: HEK293 Cyt_TAS-seq replicate 2(Ribo-)

value: NES_TadA-8e_GFP transient expression


title: HEK293T cells, NES_TadA-8e expression, treatment sample, total RNA-seq(rRNA depleted), replicate1

description: HEK293 Cyt_TAS-seq replicate 1(Ribo-)


title: HEK293T cells, TadA-8e depletion, control sample, total RNA-seq(rRNA depleted), replicate2

description: HEK293 Ctl_TAS-seq replicate 2(Ribo-)


title: HEK293T cells, ERM_TadA-8e expression, treatment sample, poly(A) RNA-seq, replicate2

description: HEK293 ERM_TAS-seq replicate 2(PolyA+)

value: ERM_TadA-8e_GFP transient expression


title: HEK293T cells, TadA-8e depletion, control sample, total RNA-seq(rRNA depleted), replicate1

description: HEK293 Ctl_TAS-seq replicate 1(Ribo-)


title: Pmel-1 T cells, untreated, Day 7, mouse 2, H3K27Ac


title: HEK293T cells, NES_TadA-8e expression, treatment sample, total RNA-seq, replicate1

description: HEK293 Cyt_TAS-seq replicate 1(Total RNA)


title: HEK293T cells, NLS_TadA-8e expression, treatment sample, poly(A) RNA-seq, replicate2

description: HEK293 Nuc_TAS-seq replicate 2(PolyA+)

value: NLS_TadA-8e_GFP transient expression


title: HEK293T cells, ERM_TadA-8e expression, treatment sample, poly(A) RNA-seq, replicate1

description: HEK293 ERM_TAS-seq replicate 1(PolyA+)


title: HEK293T cells, NLS_TadA-8e expression, treatment sample, poly(A) RNA-seq, replicate1

description: HEK293 Nuc_TAS-seq replicate 1(PolyA+)


title: Pmel-1 T cells, DCA-treated, Day 7, mouse 1

growth_protocol: To expand Pmel-1 mouse CD8+ T cells in vitro, whole spleens were mechanically disrupted with frosted glass slides, RBC lysed, then bulk splenocytes were plated in the presence of the T cells’ cognate peptide (1uM gp100) at a concentration of 1e7 cells/mL in RPMI supplemented with 10% FBS (v/v) and 50ug/mL mouse rIL-2 at 37°C with 5% CO2 for 24 hours. After 24 hours, cells were washed with fresh RPMI and plated at a concentration of 1e6/mL with 50ug/mL IL-2. Cultures were fed daily and kept at this concentration for the duration of expansion.

extract_protocol: none provided


title: HEK293T cells, TadA-8e depletion, control sample, poly(A) RNA-seq, replicate2

description: HEK293 Ctl_TAS-seq replicate 2(PolyA+)


title: Pmel-1 T cells, untreated, Day 7, mouse 1


title: Patient4, MarcoHi,  Marco-IBA+, 006

description:
Library name: L4_MarcoHi_006 | Marco-IBA+
FFPE GeoMx sequencing

value: liver

value: healthy

value: Macrophage

value: control


title: Patient4, MarcoHi,  Marco+IBA+, 006

description:
Library name: L4_MarcoHi_006 | Marco+IBA+
FFPE GeoMx sequencing


title: HEK293T cells, NES_TadA-8e expression, treatment sample, poly(A) RNA-seq, replicate2

description: HEK293 Cyt_TAS-seq replicate 2(PolyA+)


title: delta_T9_Repica1

city: Kansas City

first: Hua

last: Li

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

data_processing:
Analysis of NGS data sets e.g. sgRNA abundance was achieved using Python-based screen processing pipeline (https://github.com/mhorlbeck/ScreenProcessing)
Assembly: hg38
Supplementary files format and content: tab-delimited text file that includes the raw count for each sgRNA in each sample (CRISPRi_growth_rawcountstable.txt) and a refernce library table (CRISPRi_v2_human_librarytable.txt)

growth_protocol: K562 cells were grown in RPMI-1640 with 25 mM HEPES, 2.0 g/L NaHCO3, 0.3 g/L L-Glutamine supplemented with 10% FBS, 2mM glutamine, 100 units/mL penicillin and 100μg/mL streptomycin

extract_protocol:
Genomic DNA was extracted using NucleoSpin Blood kits from Macherey-Nagel, following the manufacturer's instructions.
Total genomic DNA (gDNA) concentration was measured, and the corresponding number of PCR reactions were assembled to use 10 µg gDNA per reaction (~100 reactions per sample). PCR reactions were prepared with NEBNext Ultra II Q5 MasterMix, gDNA, Forward (aatgatacggcgaccaccgaGATCTACACGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAgcacaaaaggaaactcaccct), and Reverse (caagcagaagacggcatacgaGATCGACTCGGTGCCACTTTTTC) primers. Note that the underlined sequence is an Illumina barcode and varies for each sample. The following PCR conditions were used: 1. Initial denaturation for 30 seconds at 98ºC, 2. Denaturation at 98ºC for 10 seconds, 3. Annealing/extension at 65ºC for 75 seconds, 4. Repeat steps 2-3 twenty-one more times, 5. Final extension at 65ºC for 5 minutes. The PCR product was purified using SPRIselect Reagent (Beckman Coulter).
Run-type single end 50, Index length: 1x6, Sequencing primers: Read 1, custom primers (gtgtgttttgagactataaGtatcccttggagaaCCAcctTGTTG); Read 2, standard Illumina index, Spike in 20% PhiX to maintain diversity  primer

treatment_protocol: Cells transduced with sgRNAs were selected by treating them with 1 µg/ml puromycin for 3 days.

value: lymphoblast cells

value: uL16 mutant

value: Day 9


title: HEK293T cells, NES_TadA-8e expression, treatment sample, poly(A) RNA-seq, replicate1

description: HEK293 Cyt_TAS-seq replicate 1(PolyA+)


title: HEK293T cells, TadA-8e depletion, control sample, poly(A) RNA-seq, replicate1

description: HEK293 Ctl_TAS-seq replicate 1(PolyA+)


title: Patient4, MarcoHi,  Des+, 005

description:
Library name: L4_MarcoHi_005 | Des+
FFPE GeoMx sequencing

value: HSC


title: Pmel-1 T cells, untreated, Day 7, mouse 3, H3K27Ac

value: splenocytes

value: CD8+ T cell

value: B6.Cg-Thy1a/Cy Tg(TcraTcrb)8Rest/J

value: untreated

value: Day 7


title: delta_T9_Repica2


title: Patient4, MarcoHi,  Marco-IBA+, 005

description:
Library name: L4_MarcoHi_005 | Marco-IBA+
FFPE GeoMx sequencing


title: Pmel-1 T cells, DCA-treated, Day 7, mouse 1, H3K27Ac

value: H3K27Ac (Abcam)

value: dichloroacetate (DCA)


title: Pmel-1 T cells, untreated, Day 7, mouse 2


title: Patient4, MarcoHi,  Marco-IBA-Des-, 005

description:
Library name: L4_MarcoHi_005 | Else
FFPE GeoMx sequencing

value: Other


title: delta_T0_Repica1

value: Day 0


title: delta_T0_Repica2


title: Pmel-1 T cells, untreated, Day 7, mouse 1, H3K27Ac


title: Pmel-1 T cells, DCA-treated, Day 7, 3


title: wt_T9_Repica2

value: uL16 wild type


title: Patient4, MarcoHi,  Marco-IBA-Des-, 004

description:
Library name: L4_MarcoHi_004 | Else
FFPE GeoMx sequencing

value: liver

value: healthy


title: Pmel-1 T cells, DCA-treated, Day 7, 2


title: Patient4, MarcoHi,  Des+, 004

description:
Library name: L4_MarcoHi_004 | Des+
FFPE GeoMx sequencing

value: control


title: Pmel-1 T cells, untreated, Day 7, mouse 3


title: wt_T9_Repica1

value: lymphoblast cells


title: wt_T0_Repica2


title: wt_T0_Repica1


title: Patient4, MarcoHi,  Des+, 003

description:
Library name: L4_MarcoHi_003 | Des+
FFPE GeoMx sequencing


title: Patient4, MarcoHi,  Marco+IBA+, 003

description:
Library name: L4_MarcoHi_003 | Marco+IBA+
FFPE GeoMx sequencing

value: Macrophage


title: Patient4, MarcoHi,  Marco+IBA+, 005

description:
Library name: L4_MarcoHi_005 | Marco+IBA+
FFPE GeoMx sequencing


title: Patients 063, 086, 087, 088 PBMCs

city: Chicago

first: Huiping

last: Liu

state: IL

address: 303 E Superior St Room 5-250

department: Pharmacology

institute: Northwestern University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMCs

extract_protocol:
White blood cells from convalescent COVID-19 patients were isolated from whole blood samples. Monocytes and Tregs were labeled with appropriate fluorescent antibodies and sorted using FACS.
Patient cells were labeled with a hashtag barcode oligo and libraries were prepared per manufacturer's instructions. Briefly, Cells were loaded onto a 10X Chromium controller, and librray was constructed using 10X chromium Next GEM Single Cell 5' Library and gel bead kits (v1.1)

value: PBMCs


title: Patients 093, 094, 095, 096 PBMCs


title: Patient 099 PBMCs


title: Patient4, MarcoHi,  Marco-IBA-Des-, 003

description:
Library name: L4_MarcoHi_003 | Else
FFPE GeoMx sequencing


title: Pateints 089, 090, 091, 092 PBMCs


title: Patients 074, 075, 076, 077 PBMCs


title: Patient4, MarcoHi,  Marco+IBA+, 002

description:
Library name: L4_MarcoHi_002 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient 106 Monocytes and Tregs and PBMCs

source_name: Monocytes and Tregs, PBMCs

value: Monocytes and Tregs, PBMCs


title: Pateints 033, 034 PBMCs


title: Patient4, MarcoHi,  Marco-IBA-Des-, 002

description:
Library name: L4_MarcoHi_002 | Else
FFPE GeoMx sequencing


title: Patient4, MarcoHi,  Des+, 001

description:
Library name: L4_MarcoHi_001 | Des+
FFPE GeoMx sequencing

value: HSC


title: Patient4, MarcoHi,  Marco-IBA-Des-, 001

description:
Library name: L4_MarcoHi_001 | Else
FFPE GeoMx sequencing


title: Patient4, MarcoHi,  Marco-IBA+, 003

description:
Library name: L4_MarcoHi_003 | Marco-IBA+
FFPE GeoMx sequencing


title: Patient 099 Monocytes and Tregs

source_name: Monocytes and Tregs

value: Monocytes and Tregs


title: Patient4, MarcoHi,  Marco+IBA+, 001

description:
Library name: L4_MarcoHi_001 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient4, MarcoHi,  Marco-IBA+, 004

description:
Library name: L4_MarcoHi_004 | Marco-IBA+
FFPE GeoMx sequencing


title: Patient4, MarcoHi,  Marco+IBA+, 004

description:
Library name: L4_MarcoHi_004 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient4, MarcoLo, Marco-IBA-Des-, 001

description:
Library name: L4_Marco | Else
FFPE GeoMx sequencing


title: Patient4, MarcoLo, Des+, 001

description:
Library name: L4_Marco | Des+
FFPE GeoMx sequencing


title: Con-3

city: Tianjin

first: Liyan

last: Zhou

address: Huanhu West Road

institute: Tianjin Medical University Cancer Institute and hospital

data_processing:
Solexa pipeline version 1.8 (Oﬀ-Line Base Caller software, version 1.8) was used for image processing and base identification.
FastQCv 0.11.7  evaluate the sequencing quality of reads.
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2 v 2.1.0.
Read count extraction and normalization were performed using StringTie v 1.3.3.
Assembly: hg19
Supplementary files format and content: Differentially_Expressed_Genes.xlsx

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Trizol-RNA Extraction (Takara). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq SR Cluster Kit v3-cBot-HS following manufacturer's protocols.

treatment_protocol: MDA-MB-231 cells were treated with 100 μg/ml AGEs or BSA for 72 h.

value: MDA-MB-231 cells

value: breast cancer cells

value: WT

value: BSA


title: Con-2


title: Con-1


title: AGEs-3

value: AGEs


title: Pateint 105 PBMCs


title: Patient4, MarcoHi,  Des+, 002

description:
Library name: L4_MarcoHi_002 | Des+
FFPE GeoMx sequencing


title: AGEs-2


title: Patient 105 Monocytes and Tregs


title: Patient3, MarcoLo,  Marco-IBA-Des-, 013

description:
Library name: L3_MarcoLo_013 | Else
FFPE GeoMx sequencing

value: fibrosis

value: Other

value: treated CCl4


title: Patient4, MarcoHi,  Marco-IBA+, 001

description:
Library name: L4_MarcoHi_001 | Marco-IBA+
FFPE GeoMx sequencing

value: liver


title: i3Neuron TDP-43 knockdown (30 days) - Knockdown 6

city: Leuven

first: Sam

last: Bryce-Smith

address: Herestraat 49

department: VIB-KU Leuven Center for Brain and Disease Research

country: Belgium

institute: KU Leuven

description:
Library name: TDP-6
Human iPS cells used in this study were engineered from WTC11 line to express mouse or human neurogenin-2 under a doxycycline-inducible promoter (Fernandopulle et al., Current Protocols in Cell Biology, 2018; Wang et al., Stem Cell Reports, 2017) and an enzymatically dead Cas9 (+/- CAG-dCas9-BFP-KRAB) at safe-harbour loci (Tian et al., Neuron, 2019). CRISPRi  knockdown of TDP-43 in iPSCs was achieved  using  sgRNA  targeting  the  transcription  start  site  of  TARDBP (GGGAAGTCAGCCGTGAGACC) or a non-targeting control (GTCCACCCTTATCTAGGCTA), delivered by lentiviral transduction. i3Neurons  were  induced  as previously  described (Fernandopulle et al., Current Protocols in Cell Biology, 2018)  with  the  addition  of  SMAD  and  WNT  inhibitors  (Nehme et al., Cell Reports, 2018)(SB431542  10  µM; LDN-193189  100  nM;  XAV939  2  µM  all  from  Cambridge  Biosciences). After  induction,  cells were cultured in BrainPhys Media (StemCell  Technologies) with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1x N2 supplement (Thermo  Fisher), 1  x B27 supplement (Thermo Fisher), 200 nM Ascorbic Acid (Sigma), 1 mM dibutyryl cyclic-AMP (Sigma) and 1 µg/ml Laminin (Thermo  Fisher) as previously  described (Bardy et al., PNAS, 2015) and harvested 30 days after differentiation. Strand-specific, poly(A) enriched sequencing libraries dataset were prepared using the Kapa mRNA Hyper Prep kit. 100ng total RNA was used as input material for poly(A)+ mRNA capture. Fragmentation was performed for 6 minutes at 85°C to obtain a target fragment size of 300-400bp, and 13 cycles of PCR amplification were performed. The resulting libraries were sequenced 2x150bp on the Illumina NextSeq2000 machine.

data_processing:
Samples were processed as previously described (Humphrey et al., Nat Neurosci., 2023) using the RAPiD-nf nextflow pipeline. Briefly, adapters were trimmed from raw reads using Trimmomatic v0.36, and reads were aligned to the GRCh38 genome build using gene models from GENCODE v30 with STAR v2.7.2a. The RAPiD-nf pipeline is available at https://github.com/CommonMindConsortium/RAPiD-nf/ .
Gencode v40 transcripts were quantified by Salmon using a decoy-aware transcriptome index. Salmon v1.8.0 was used with the --posBias, --gcBias and --seqBias flags enabled (otherwise default parameters). Tximport (default parameters) was used to summarise estimated transcript counts to the gene-level and produce raw count matrices.
Assembly: hg38
Supplementary files format and content: comma-delimited text file containing raw gene counts for each sample

value: iPSC-derived cortical neuron


title: TSB807_HPGA_RW_TPCA

city: La Jolla

first: Tom

last: Suter

state: CA

address: 9500 Gilman Dr

department: Department of Medicine

institute: UCSD

data_processing:
Construction of contact matrices   Reads pairs obtained by sequencing the Hi-C libraries were mapped to the human reference genome assembly hg18 using bowtie2 version 2.3.0 with the following parameters: --end-to-end --very-sensitive -L 30 --score-min L,-0.6,-0.2 --mp 6,2. For each pair, each 50-base read was mapped independently. Reads aligning to multiple genomic locations were discarded. Reads that could not be aligned to any genomic location were further processed as follows. The 8-base sequence expected for the junction resulting from ligation of the blunt ends of two Hi-C fragments was searched within the read sequence, allowing for a single base mismatch. If the searched junction sequence was found, then the read sequence was split at the midpoint of the junction and the resulting sub-sequences were mapped independently to the reference genome. If the junction sequence was not found, then the read sequence was processed in a manner similar to the iterative mapping procedure of Imakaev et al (Imakaev 2012). Sub-sequences starting from each end of the read were iteratively extracted and independently mapped to the reference genome. The initial length of each sub-sequence was 16 bases and was incremented by 5 bases until the sub-sequence did not align to multiple genomic locations. All read sequences and sub-sequences that successfully aligned to unique genomic locations were then grouped by read pair of origin. Groups of size greater than one were analyzed to infer pairs of read sequences, or sub-sequences, that likely resulted from pairs of cross-linked Hi-C fragments. For each inferred sequence pair, the two alignment coordinates were used to filter out duplicated pairs, likely resulting from PCR amplification, and spurious intra-chromosomal interactions, likely resulting from dangling ends and self-ligation products, as described by Jin F et al (Jin 2013). Specifically, sequence pairs aligned to genomic locations closer than 500 bp were classified as “samestrand” and “outward” pairs and hence discarded. The remaining aligned sequence pairs were used to generate symmetric matrices of raw contacts counts for all possible pairs of genomic bins, with one matrix per chromosome and 250 kb per bin. The contact matrices were pruned by removing rows and columns that contained too many zero entries in all of the samples considered. The minimum acceptable number of non-zero entries was arbitrarily chosen to be 25% of the median number of non-zero entries in each row. To remove experimental biases, the resulting contact matrices were processed with the iterative matrix-balancing procedure of Imakaev et al (Imakaev 2012).
Genome_build: hg18
Supplementary_files_format_and_content: compressed set of .tsv files for each chromosome: each .tsv file contains contact counts for each chromosome, binned into 500000bp bins

source_name: Foreskin dermal fibroblast

growth_protocol: BJ fibroblasts (ATCC® CRL-2522) were cultured at 37 °C in 20% O2 and 5% CO2 in 4.5 g/L DMEM (Gibco 10566-016) in 10% FBS.  Cell lines were initially plated at PD26, grown to confluence, and then split 1:8.  Population doubling was recorded and incremented by 3 upon each 1:4 8 split.  BJ fibroblasts were considered to be “young” when collected below population doubling (PD) 35, intermediate fibroblasts were harvested between PD 35-50, and fibroblasts were considered to be senescent when cells failed to divide after at least one week of passaging, which typically occurred after at least PD64 and was initially confirmed using beta galactosidase staining.  To mitigate the effects of cell cycle upon our results, non-senescent, still dividing fibroblasts were grown to confluence prior to harvesting for any experiments, in order to ensure contact inhibited quiescence and similar growth arrest among all populations of cells.  Cells grown in rapamycin were introduced to and maintained in 10nM rapamycin after recovery from thawing while still at a young state.  For rapamycin withdrawal experiments, rapamycin maintained cells were grown to arrest, which typically occurred between PD75-85.  These cells are termed High Passage Growth Arrested.  At this point, the cells were divided into two plates that were either maintained or withdrawn from rapamycin for 2 weeks until they were collected.

extract_protocol:
In-Situ Hi-C was performed as described in Rao et al., 2014 (Rao et al., 2014).  In brief, approximately 1 million BJ fibroblasts (senescent or quiescent via contact inhibition) per experimental condition were collected and treated overnight in MboI restriction enzyme at 37°C rotating at 8 RPM.  Nuclei were then Klenow treated in the presence of biotin-CTP in order to both blunt and biotin label the digested chromatin.  Nuclei were then treated with HC T4 DNA ligase (Enzymatics) to perform in-situ ligation.  Ligated chromatin was then extracted and purified from nuclei via incubation in SDS followed by phenol/chloroform/isoamyl alcohol extraction.
Isolated chromatin was then sheared to ~300bp using Covaris sonication and the associated manufacturer’s protocol, afterwards fragments >400bp were removed via size selection using AmPure XP bead selection (Beckman-A63880).  Extracted chromatin fragments were then attached to Dynabeads MyOne Streptavidin T1 (ThermoFisher Scientific-65601), and were then reblunted via Klenow, followed by poly-A tailing via Exo-Klenow treatment, both reactions on beads.  Illumina TruSeq adapters were ligated to the bead attached chromatin fragments via treatment with HC T4 DNA ligase, after which the library was PCR amplified using NEBNext High Fidelity 2x PCR Master Mix (NEB-M0541S) and Illumina TruSeq amplification primers.  The library was again size-selected via AmPure beads and sequenced using the HiSeq 4000 using 50 cycle paired end runs.

treatment_protocol: Cells grown in rapamycin were introduced to and maintained in 10nM rapamycin after recovery from thawing.  Rapamycin maintained cells were collected for ChIP-seq at PD31 and PD66 to correspond with similar PD young and senescent DMSO treated cells.  High Passage Growth Arrested BJ fibroblasts maintained in 10nM rapamycin were then either maintained or withdrawn from rapamycin for 14 additional days, and treated with either control or the IKK/p65 inhibitor TPCA-1 (500nM) during this 14 day period.

value: BJ Fibroblast

tag: Stage

value: HPGA

value: Rapamycin Withdrawn + TPCA


title: i3Neuron TDP-43 knockdown (30 days) - Knockdown 5

description:
Library name: TDP-5
Human iPS cells used in this study were engineered from WTC11 line to express mouse or human neurogenin-2 under a doxycycline-inducible promoter (Fernandopulle et al., Current Protocols in Cell Biology, 2018; Wang et al., Stem Cell Reports, 2017) and an enzymatically dead Cas9 (+/- CAG-dCas9-BFP-KRAB) at safe-harbour loci (Tian et al., Neuron, 2019). CRISPRi  knockdown of TDP-43 in iPSCs was achieved  using  sgRNA  targeting  the  transcription  start  site  of  TARDBP (GGGAAGTCAGCCGTGAGACC) or a non-targeting control (GTCCACCCTTATCTAGGCTA), delivered by lentiviral transduction. i3Neurons  were  induced  as previously  described (Fernandopulle et al., Current Protocols in Cell Biology, 2018)  with  the  addition  of  SMAD  and  WNT  inhibitors  (Nehme et al., Cell Reports, 2018)(SB431542  10  µM; LDN-193189  100  nM;  XAV939  2  µM  all  from  Cambridge  Biosciences). After  induction,  cells were cultured in BrainPhys Media (StemCell  Technologies) with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1x N2 supplement (Thermo  Fisher), 1  x B27 supplement (Thermo Fisher), 200 nM Ascorbic Acid (Sigma), 1 mM dibutyryl cyclic-AMP (Sigma) and 1 µg/ml Laminin (Thermo  Fisher) as previously  described (Bardy et al., PNAS, 2015) and harvested 30 days after differentiation. Strand-specific, poly(A) enriched sequencing libraries dataset were prepared using the Kapa mRNA Hyper Prep kit. 100ng total RNA was used as input material for poly(A)+ mRNA capture. Fragmentation was performed for 6 minutes at 85°C to obtain a target fragment size of 300-400bp, and 13 cycles of PCR amplification were performed. The resulting libraries were sequenced 2x150bp on the Illumina NextSeq2000 machine.


title: TSB805_HPGA_RM

value: Rapamycin Maintained


title: Patient3, MarcoLo,  Des+, 013

description:
Library name: L3_MarcoLo_013 | Des+
FFPE GeoMx sequencing


title: i3Neuron TDP-43 knockdown (30 days) - Knockdown 4

description:
Library name: TDP-4
Human iPS cells used in this study were engineered from WTC11 line to express mouse or human neurogenin-2 under a doxycycline-inducible promoter (Fernandopulle et al., Current Protocols in Cell Biology, 2018; Wang et al., Stem Cell Reports, 2017) and an enzymatically dead Cas9 (+/- CAG-dCas9-BFP-KRAB) at safe-harbour loci (Tian et al., Neuron, 2019). CRISPRi  knockdown of TDP-43 in iPSCs was achieved  using  sgRNA  targeting  the  transcription  start  site  of  TARDBP (GGGAAGTCAGCCGTGAGACC) or a non-targeting control (GTCCACCCTTATCTAGGCTA), delivered by lentiviral transduction. i3Neurons  were  induced  as previously  described (Fernandopulle et al., Current Protocols in Cell Biology, 2018)  with  the  addition  of  SMAD  and  WNT  inhibitors  (Nehme et al., Cell Reports, 2018)(SB431542  10  µM; LDN-193189  100  nM;  XAV939  2  µM  all  from  Cambridge  Biosciences). After  induction,  cells were cultured in BrainPhys Media (StemCell  Technologies) with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1x N2 supplement (Thermo  Fisher), 1  x B27 supplement (Thermo Fisher), 200 nM Ascorbic Acid (Sigma), 1 mM dibutyryl cyclic-AMP (Sigma) and 1 µg/ml Laminin (Thermo  Fisher) as previously  described (Bardy et al., PNAS, 2015) and harvested 30 days after differentiation. Strand-specific, poly(A) enriched sequencing libraries dataset were prepared using the Kapa mRNA Hyper Prep kit. 100ng total RNA was used as input material for poly(A)+ mRNA capture. Fragmentation was performed for 6 minutes at 85°C to obtain a target fragment size of 300-400bp, and 13 cycles of PCR amplification were performed. The resulting libraries were sequenced 2x150bp on the Illumina NextSeq2000 machine.


title: AGEs-1


title: i3Neuron TDP-43 knockdown (30 days) - Knockdown 2

description:
Library name: TDP-2
Human iPS cells used in this study were engineered from WTC11 line to express mouse or human neurogenin-2 under a doxycycline-inducible promoter (Fernandopulle et al., Current Protocols in Cell Biology, 2018; Wang et al., Stem Cell Reports, 2017) and an enzymatically dead Cas9 (+/- CAG-dCas9-BFP-KRAB) at safe-harbour loci (Tian et al., Neuron, 2019). CRISPRi  knockdown of TDP-43 in iPSCs was achieved  using  sgRNA  targeting  the  transcription  start  site  of  TARDBP (GGGAAGTCAGCCGTGAGACC) or a non-targeting control (GTCCACCCTTATCTAGGCTA), delivered by lentiviral transduction. i3Neurons  were  induced  as previously  described (Fernandopulle et al., Current Protocols in Cell Biology, 2018)  with  the  addition  of  SMAD  and  WNT  inhibitors  (Nehme et al., Cell Reports, 2018)(SB431542  10  µM; LDN-193189  100  nM;  XAV939  2  µM  all  from  Cambridge  Biosciences). After  induction,  cells were cultured in BrainPhys Media (StemCell  Technologies) with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1x N2 supplement (Thermo  Fisher), 1  x B27 supplement (Thermo Fisher), 200 nM Ascorbic Acid (Sigma), 1 mM dibutyryl cyclic-AMP (Sigma) and 1 µg/ml Laminin (Thermo  Fisher) as previously  described (Bardy et al., PNAS, 2015) and harvested 30 days after differentiation. Strand-specific, poly(A) enriched sequencing libraries dataset were prepared using the Kapa mRNA Hyper Prep kit. 100ng total RNA was used as input material for poly(A)+ mRNA capture. Fragmentation was performed for 6 minutes at 85°C to obtain a target fragment size of 300-400bp, and 13 cycles of PCR amplification were performed. The resulting libraries were sequenced 2x150bp on the Illumina NextSeq2000 machine.


title: TSB803_Young_PD31_Rapa

value: Young - PD31 - Quiescent

value: Rapamycin


title: TSB804_PD66_Rapa

value: PD66 - Quiescent


title: TSB802_Senescent_PD66_DMSO

value: Senescent - PD66

value: DMSO


title: TSB801_Young_PD31_DMSO


title: i3Neuron TDP-43 knockdown (30 days) - Knockdown 1

description:
Library name: TDP-1
Human iPS cells used in this study were engineered from WTC11 line to express mouse or human neurogenin-2 under a doxycycline-inducible promoter (Fernandopulle et al., Current Protocols in Cell Biology, 2018; Wang et al., Stem Cell Reports, 2017) and an enzymatically dead Cas9 (+/- CAG-dCas9-BFP-KRAB) at safe-harbour loci (Tian et al., Neuron, 2019). CRISPRi  knockdown of TDP-43 in iPSCs was achieved  using  sgRNA  targeting  the  transcription  start  site  of  TARDBP (GGGAAGTCAGCCGTGAGACC) or a non-targeting control (GTCCACCCTTATCTAGGCTA), delivered by lentiviral transduction. i3Neurons  were  induced  as previously  described (Fernandopulle et al., Current Protocols in Cell Biology, 2018)  with  the  addition  of  SMAD  and  WNT  inhibitors  (Nehme et al., Cell Reports, 2018)(SB431542  10  µM; LDN-193189  100  nM;  XAV939  2  µM  all  from  Cambridge  Biosciences). After  induction,  cells were cultured in BrainPhys Media (StemCell  Technologies) with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1x N2 supplement (Thermo  Fisher), 1  x B27 supplement (Thermo Fisher), 200 nM Ascorbic Acid (Sigma), 1 mM dibutyryl cyclic-AMP (Sigma) and 1 µg/ml Laminin (Thermo  Fisher) as previously  described (Bardy et al., PNAS, 2015) and harvested 30 days after differentiation. Strand-specific, poly(A) enriched sequencing libraries dataset were prepared using the Kapa mRNA Hyper Prep kit. 100ng total RNA was used as input material for poly(A)+ mRNA capture. Fragmentation was performed for 6 minutes at 85°C to obtain a target fragment size of 300-400bp, and 13 cycles of PCR amplification were performed. The resulting libraries were sequenced 2x150bp on the Illumina NextSeq2000 machine.


title: i3Neuron TDP-43 knockdown (30 days) - Control 6

description:
Library name: CTRL-6
Human iPS cells used in this study were engineered from WTC11 line to express mouse or human neurogenin-2 under a doxycycline-inducible promoter (Fernandopulle et al., Current Protocols in Cell Biology, 2018; Wang et al., Stem Cell Reports, 2017) and an enzymatically dead Cas9 (+/- CAG-dCas9-BFP-KRAB) at safe-harbour loci (Tian et al., Neuron, 2019). CRISPRi  knockdown of TDP-43 in iPSCs was achieved  using  sgRNA  targeting  the  transcription  start  site  of  TARDBP (GGGAAGTCAGCCGTGAGACC) or a non-targeting control (GTCCACCCTTATCTAGGCTA), delivered by lentiviral transduction. i3Neurons  were  induced  as previously  described (Fernandopulle et al., Current Protocols in Cell Biology, 2018)  with  the  addition  of  SMAD  and  WNT  inhibitors  (Nehme et al., Cell Reports, 2018)(SB431542  10  µM; LDN-193189  100  nM;  XAV939  2  µM  all  from  Cambridge  Biosciences). After  induction,  cells were cultured in BrainPhys Media (StemCell  Technologies) with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1x N2 supplement (Thermo  Fisher), 1  x B27 supplement (Thermo Fisher), 200 nM Ascorbic Acid (Sigma), 1 mM dibutyryl cyclic-AMP (Sigma) and 1 µg/ml Laminin (Thermo  Fisher) as previously  described (Bardy et al., PNAS, 2015) and harvested 30 days after differentiation. Strand-specific, poly(A) enriched sequencing libraries dataset were prepared using the Kapa mRNA Hyper Prep kit. 100ng total RNA was used as input material for poly(A)+ mRNA capture. Fragmentation was performed for 6 minutes at 85°C to obtain a target fragment size of 300-400bp, and 13 cycles of PCR amplification were performed. The resulting libraries were sequenced 2x150bp on the Illumina NextSeq2000 machine.


title: i3Neuron TDP-43 knockdown (30 days) - Control 4

description:
Library name: CTRL-4
Human iPS cells used in this study were engineered from WTC11 line to express mouse or human neurogenin-2 under a doxycycline-inducible promoter (Fernandopulle et al., Current Protocols in Cell Biology, 2018; Wang et al., Stem Cell Reports, 2017) and an enzymatically dead Cas9 (+/- CAG-dCas9-BFP-KRAB) at safe-harbour loci (Tian et al., Neuron, 2019). CRISPRi  knockdown of TDP-43 in iPSCs was achieved  using  sgRNA  targeting  the  transcription  start  site  of  TARDBP (GGGAAGTCAGCCGTGAGACC) or a non-targeting control (GTCCACCCTTATCTAGGCTA), delivered by lentiviral transduction. i3Neurons  were  induced  as previously  described (Fernandopulle et al., Current Protocols in Cell Biology, 2018)  with  the  addition  of  SMAD  and  WNT  inhibitors  (Nehme et al., Cell Reports, 2018)(SB431542  10  µM; LDN-193189  100  nM;  XAV939  2  µM  all  from  Cambridge  Biosciences). After  induction,  cells were cultured in BrainPhys Media (StemCell  Technologies) with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1x N2 supplement (Thermo  Fisher), 1  x B27 supplement (Thermo Fisher), 200 nM Ascorbic Acid (Sigma), 1 mM dibutyryl cyclic-AMP (Sigma) and 1 µg/ml Laminin (Thermo  Fisher) as previously  described (Bardy et al., PNAS, 2015) and harvested 30 days after differentiation. Strand-specific, poly(A) enriched sequencing libraries dataset were prepared using the Kapa mRNA Hyper Prep kit. 100ng total RNA was used as input material for poly(A)+ mRNA capture. Fragmentation was performed for 6 minutes at 85°C to obtain a target fragment size of 300-400bp, and 13 cycles of PCR amplification were performed. The resulting libraries were sequenced 2x150bp on the Illumina NextSeq2000 machine.


title: SH-SY5Y TDP-43 knockdown with cycloheximide treatment - TDP-43 knockdown no cycloheximide - 2

description:
Library name: SHSY5Y_DOX_CTRL_2
SH-SY5Y cells were transduced with a SmartVector lentivirus (V3IHSHEG_6494503) containing a doxycycline-inducible shRNA cassette for TDP-43. Transduced cells were selected with puromycin (1 μg/ml) for one week, before being plated as single cells and expanded to obtain a clonal population. Cells were grown in DMEM/F12 + Glutamax (Thermo) supplemented with 10% FBS (Thermo) and 1% PenStrep (Thermo). For induction of shRNA against TDP-43, cells were treated with 25 ng/ml doxycyline hyclate (Sigma). After 10 days, cells were treated  either with 100 µM cycloheximide (CHX) or DMSO (Pereverzev et al., 2015) for 6 h before isolating the RNA. Overall, 4 conditions were generated: Control for TDP-43 knockdown and DMSO (control/control), Control for TDP-43 knockdown and CHX-treated (control/CHX), Positive for TDP-43 knockdown and DMSO (TDP43/control) and Positive for TDP-43 knockdown and CHX-treated (TDP43/CHX). RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s protocol, including the on-column DNA digestion step.  RNA concentrations were measured by Nanodrop and 1,000 ng of RNA was used for reverse transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x100bp, > 40 million reads per sample).

data_processing:
Raw reads in FASTQ format were quality trimmed for a minimum Phred score of 10 and otherwise default parameters using fastp (v0.20.1). Quality trimmed reads were aligned to the GRCh38 genome build using gene models from GENCODE v40 with STAR (v2.7.8a).  The  alignment  pipeline is implemented in Snakemake and is available at  https://github.com/frattalab/rna_seq_snakemake  .
Gencode v40 transcripts were quantified by Salmon using a decoy-aware transcriptome index. Salmon v1.8.0 was used with the --posBias, --gcBias and --seqBias flags enabled (otherwise default parameters). Tximport (default parameters) was used to summarise estimated transcript counts to the gene-level and produce raw count matrices.
Assembly: hg38
Supplementary files format and content: comma-delimited text file containing raw gene counts for each sample

extract_protocol:
RNA  was  extracted using  the  RNeasy  mini  kit  (Qiagen)  following  the  manufacturer’s  protocol,  including  the on-column  DNA  digestion  step.  RNA  concentrations  were  measured  by  Nanodrop  and  1,000  ng of  RNA  was  used  for  reverse  transcription.
Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (iPSC-derived cortical neurons = 2x150bp, > 40 million reads per sample, SH-SY5Y = 2x100bp, > 40 million reads per sample).

value: neuroblast


title: i3Neuron TDP-43 knockdown (30 days) - Control 3

description:
Library name: CTRL-3
Human iPS cells used in this study were engineered from WTC11 line to express mouse or human neurogenin-2 under a doxycycline-inducible promoter (Fernandopulle et al., Current Protocols in Cell Biology, 2018; Wang et al., Stem Cell Reports, 2017) and an enzymatically dead Cas9 (+/- CAG-dCas9-BFP-KRAB) at safe-harbour loci (Tian et al., Neuron, 2019). CRISPRi  knockdown of TDP-43 in iPSCs was achieved  using  sgRNA  targeting  the  transcription  start  site  of  TARDBP (GGGAAGTCAGCCGTGAGACC) or a non-targeting control (GTCCACCCTTATCTAGGCTA), delivered by lentiviral transduction. i3Neurons  were  induced  as previously  described (Fernandopulle et al., Current Protocols in Cell Biology, 2018)  with  the  addition  of  SMAD  and  WNT  inhibitors  (Nehme et al., Cell Reports, 2018)(SB431542  10  µM; LDN-193189  100  nM;  XAV939  2  µM  all  from  Cambridge  Biosciences). After  induction,  cells were cultured in BrainPhys Media (StemCell  Technologies) with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1x N2 supplement (Thermo  Fisher), 1  x B27 supplement (Thermo Fisher), 200 nM Ascorbic Acid (Sigma), 1 mM dibutyryl cyclic-AMP (Sigma) and 1 µg/ml Laminin (Thermo  Fisher) as previously  described (Bardy et al., PNAS, 2015) and harvested 30 days after differentiation. Strand-specific, poly(A) enriched sequencing libraries dataset were prepared using the Kapa mRNA Hyper Prep kit. 100ng total RNA was used as input material for poly(A)+ mRNA capture. Fragmentation was performed for 6 minutes at 85°C to obtain a target fragment size of 300-400bp, and 13 cycles of PCR amplification were performed. The resulting libraries were sequenced 2x150bp on the Illumina NextSeq2000 machine.


title: i3Neuron TDP-43 knockdown (30 days) - Knockdown 3

description:
Library name: TDP-3
Human iPS cells used in this study were engineered from WTC11 line to express mouse or human neurogenin-2 under a doxycycline-inducible promoter (Fernandopulle et al., Current Protocols in Cell Biology, 2018; Wang et al., Stem Cell Reports, 2017) and an enzymatically dead Cas9 (+/- CAG-dCas9-BFP-KRAB) at safe-harbour loci (Tian et al., Neuron, 2019). CRISPRi  knockdown of TDP-43 in iPSCs was achieved  using  sgRNA  targeting  the  transcription  start  site  of  TARDBP (GGGAAGTCAGCCGTGAGACC) or a non-targeting control (GTCCACCCTTATCTAGGCTA), delivered by lentiviral transduction. i3Neurons  were  induced  as previously  described (Fernandopulle et al., Current Protocols in Cell Biology, 2018)  with  the  addition  of  SMAD  and  WNT  inhibitors  (Nehme et al., Cell Reports, 2018)(SB431542  10  µM; LDN-193189  100  nM;  XAV939  2  µM  all  from  Cambridge  Biosciences). After  induction,  cells were cultured in BrainPhys Media (StemCell  Technologies) with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1x N2 supplement (Thermo  Fisher), 1  x B27 supplement (Thermo Fisher), 200 nM Ascorbic Acid (Sigma), 1 mM dibutyryl cyclic-AMP (Sigma) and 1 µg/ml Laminin (Thermo  Fisher) as previously  described (Bardy et al., PNAS, 2015) and harvested 30 days after differentiation. Strand-specific, poly(A) enriched sequencing libraries dataset were prepared using the Kapa mRNA Hyper Prep kit. 100ng total RNA was used as input material for poly(A)+ mRNA capture. Fragmentation was performed for 6 minutes at 85°C to obtain a target fragment size of 300-400bp, and 13 cycles of PCR amplification were performed. The resulting libraries were sequenced 2x150bp on the Illumina NextSeq2000 machine.


title: i3Neuron TDP-43 knockdown (30 days) - Control 5

description:
Library name: CTRL-5
Human iPS cells used in this study were engineered from WTC11 line to express mouse or human neurogenin-2 under a doxycycline-inducible promoter (Fernandopulle et al., Current Protocols in Cell Biology, 2018; Wang et al., Stem Cell Reports, 2017) and an enzymatically dead Cas9 (+/- CAG-dCas9-BFP-KRAB) at safe-harbour loci (Tian et al., Neuron, 2019). CRISPRi  knockdown of TDP-43 in iPSCs was achieved  using  sgRNA  targeting  the  transcription  start  site  of  TARDBP (GGGAAGTCAGCCGTGAGACC) or a non-targeting control (GTCCACCCTTATCTAGGCTA), delivered by lentiviral transduction. i3Neurons  were  induced  as previously  described (Fernandopulle et al., Current Protocols in Cell Biology, 2018)  with  the  addition  of  SMAD  and  WNT  inhibitors  (Nehme et al., Cell Reports, 2018)(SB431542  10  µM; LDN-193189  100  nM;  XAV939  2  µM  all  from  Cambridge  Biosciences). After  induction,  cells were cultured in BrainPhys Media (StemCell  Technologies) with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1x N2 supplement (Thermo  Fisher), 1  x B27 supplement (Thermo Fisher), 200 nM Ascorbic Acid (Sigma), 1 mM dibutyryl cyclic-AMP (Sigma) and 1 µg/ml Laminin (Thermo  Fisher) as previously  described (Bardy et al., PNAS, 2015) and harvested 30 days after differentiation. Strand-specific, poly(A) enriched sequencing libraries dataset were prepared using the Kapa mRNA Hyper Prep kit. 100ng total RNA was used as input material for poly(A)+ mRNA capture. Fragmentation was performed for 6 minutes at 85°C to obtain a target fragment size of 300-400bp, and 13 cycles of PCR amplification were performed. The resulting libraries were sequenced 2x150bp on the Illumina NextSeq2000 machine.


title: SH-SY5Y TDP-43 knockdown with cycloheximide treatment - TDP-43 knockdown no cycloheximide - 3

description:
Library name: SHSY5Y_DOX_CTRL_3
SH-SY5Y cells were transduced with a SmartVector lentivirus (V3IHSHEG_6494503) containing a doxycycline-inducible shRNA cassette for TDP-43. Transduced cells were selected with puromycin (1 μg/ml) for one week, before being plated as single cells and expanded to obtain a clonal population. Cells were grown in DMEM/F12 + Glutamax (Thermo) supplemented with 10% FBS (Thermo) and 1% PenStrep (Thermo). For induction of shRNA against TDP-43, cells were treated with 25 ng/ml doxycyline hyclate (Sigma). After 10 days, cells were treated  either with 100 µM cycloheximide (CHX) or DMSO (Pereverzev et al., 2015) for 6 h before isolating the RNA. Overall, 4 conditions were generated: Control for TDP-43 knockdown and DMSO (control/control), Control for TDP-43 knockdown and CHX-treated (control/CHX), Positive for TDP-43 knockdown and DMSO (TDP43/control) and Positive for TDP-43 knockdown and CHX-treated (TDP43/CHX). RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s protocol, including the on-column DNA digestion step.  RNA concentrations were measured by Nanodrop and 1,000 ng of RNA was used for reverse transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x100bp, > 40 million reads per sample).


title: i3Neuron TDP-43 knockdown (30 days) - Control 2

description:
Library name: CTRL-2
Human iPS cells used in this study were engineered from WTC11 line to express mouse or human neurogenin-2 under a doxycycline-inducible promoter (Fernandopulle et al., Current Protocols in Cell Biology, 2018; Wang et al., Stem Cell Reports, 2017) and an enzymatically dead Cas9 (+/- CAG-dCas9-BFP-KRAB) at safe-harbour loci (Tian et al., Neuron, 2019). CRISPRi  knockdown of TDP-43 in iPSCs was achieved  using  sgRNA  targeting  the  transcription  start  site  of  TARDBP (GGGAAGTCAGCCGTGAGACC) or a non-targeting control (GTCCACCCTTATCTAGGCTA), delivered by lentiviral transduction. i3Neurons  were  induced  as previously  described (Fernandopulle et al., Current Protocols in Cell Biology, 2018)  with  the  addition  of  SMAD  and  WNT  inhibitors  (Nehme et al., Cell Reports, 2018)(SB431542  10  µM; LDN-193189  100  nM;  XAV939  2  µM  all  from  Cambridge  Biosciences). After  induction,  cells were cultured in BrainPhys Media (StemCell  Technologies) with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1x N2 supplement (Thermo  Fisher), 1  x B27 supplement (Thermo Fisher), 200 nM Ascorbic Acid (Sigma), 1 mM dibutyryl cyclic-AMP (Sigma) and 1 µg/ml Laminin (Thermo  Fisher) as previously  described (Bardy et al., PNAS, 2015) and harvested 30 days after differentiation. Strand-specific, poly(A) enriched sequencing libraries dataset were prepared using the Kapa mRNA Hyper Prep kit. 100ng total RNA was used as input material for poly(A)+ mRNA capture. Fragmentation was performed for 6 minutes at 85°C to obtain a target fragment size of 300-400bp, and 13 cycles of PCR amplification were performed. The resulting libraries were sequenced 2x150bp on the Illumina NextSeq2000 machine.


title: Patient4, MarcoLo, Marco-IBA+, 001

description:
Library name: L4_Marco | Marco-IBA+
FFPE GeoMx sequencing

value: healthy

value: Macrophage

value: control


title: SH-SY5Y TDP-43 knockdown with cycloheximide treatment - TDP-43 control no cycloheximide - 4

description:
Library name: SHSY5Y_CTRL_CTRL_4
SH-SY5Y cells were transduced with a SmartVector lentivirus (V3IHSHEG_6494503) containing a doxycycline-inducible shRNA cassette for TDP-43. Transduced cells were selected with puromycin (1 μg/ml) for one week, before being plated as single cells and expanded to obtain a clonal population. Cells were grown in DMEM/F12 + Glutamax (Thermo) supplemented with 10% FBS (Thermo) and 1% PenStrep (Thermo). For induction of shRNA against TDP-43, cells were treated with 25 ng/ml doxycyline hyclate (Sigma). After 10 days, cells were treated  either with 100 µM cycloheximide (CHX) or DMSO (Pereverzev et al., 2015) for 6 h before isolating the RNA. Overall, 4 conditions were generated: Control for TDP-43 knockdown and DMSO (control/control), Control for TDP-43 knockdown and CHX-treated (control/CHX), Positive for TDP-43 knockdown and DMSO (TDP43/control) and Positive for TDP-43 knockdown and CHX-treated (TDP43/CHX). RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s protocol, including the on-column DNA digestion step.  RNA concentrations were measured by Nanodrop and 1,000 ng of RNA was used for reverse transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x100bp, > 40 million reads per sample).


title: SH-SY5Y TDP-43 knockdown with cycloheximide treatment - TDP-43 knockdown no cycloheximide - 1

description:
Library name: SHSY5Y_DOX_CTRL_1
SH-SY5Y cells were transduced with a SmartVector lentivirus (V3IHSHEG_6494503) containing a doxycycline-inducible shRNA cassette for TDP-43. Transduced cells were selected with puromycin (1 μg/ml) for one week, before being plated as single cells and expanded to obtain a clonal population. Cells were grown in DMEM/F12 + Glutamax (Thermo) supplemented with 10% FBS (Thermo) and 1% PenStrep (Thermo). For induction of shRNA against TDP-43, cells were treated with 25 ng/ml doxycyline hyclate (Sigma). After 10 days, cells were treated  either with 100 µM cycloheximide (CHX) or DMSO (Pereverzev et al., 2015) for 6 h before isolating the RNA. Overall, 4 conditions were generated: Control for TDP-43 knockdown and DMSO (control/control), Control for TDP-43 knockdown and CHX-treated (control/CHX), Positive for TDP-43 knockdown and DMSO (TDP43/control) and Positive for TDP-43 knockdown and CHX-treated (TDP43/CHX). RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s protocol, including the on-column DNA digestion step.  RNA concentrations were measured by Nanodrop and 1,000 ng of RNA was used for reverse transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x100bp, > 40 million reads per sample).


title: TSB806_HPGA_RW

value: Rapamycin Withdrawn


title: SH-SY5Y TDP-43 knockdown with cycloheximide treatment - TDP-43 control no cycloheximide - 3

description:
Library name: SHSY5Y_CTRL_CTRL_3
SH-SY5Y cells were transduced with a SmartVector lentivirus (V3IHSHEG_6494503) containing a doxycycline-inducible shRNA cassette for TDP-43. Transduced cells were selected with puromycin (1 μg/ml) for one week, before being plated as single cells and expanded to obtain a clonal population. Cells were grown in DMEM/F12 + Glutamax (Thermo) supplemented with 10% FBS (Thermo) and 1% PenStrep (Thermo). For induction of shRNA against TDP-43, cells were treated with 25 ng/ml doxycyline hyclate (Sigma). After 10 days, cells were treated  either with 100 µM cycloheximide (CHX) or DMSO (Pereverzev et al., 2015) for 6 h before isolating the RNA. Overall, 4 conditions were generated: Control for TDP-43 knockdown and DMSO (control/control), Control for TDP-43 knockdown and CHX-treated (control/CHX), Positive for TDP-43 knockdown and DMSO (TDP43/control) and Positive for TDP-43 knockdown and CHX-treated (TDP43/CHX). RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s protocol, including the on-column DNA digestion step.  RNA concentrations were measured by Nanodrop and 1,000 ng of RNA was used for reverse transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x100bp, > 40 million reads per sample).


title: TBI056_1VST_MONO

city: Chapel Hill

first: Kristina

last: De Paris

state: North Carolina

address: Mary Ellen Jones Building , 116 manning Drive

department: Department of Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

description:
Library name: TBI056_1VST_MONO
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0

data_processing:
Raw FASTAQ files after RNA sequencing were processed using the CLC Genomics Workbench 22.0 (CLC Bio, QIAGEN, Aarhus, Denmark).
The raw reads were  trimmed for universal and small RNA adaptors.
Subsequently mapped and aligned to the hg38 reference genome using built-in RNA-seq.
Differential gene expression analysis workflow in CLC genomics with default settings
Assembly: The hg38 reference genome was used to align
Supplementary files format and content: CSV files including  log2 fold change, p value and FDR value.

source_name: Monocytes

extract_protocol:
PBMC were separated by Ficoll-Hypaque gradient centrifugation and stored as viable PBMC in liquid nitrogen.Later PBMC were thawed, stained with anti-CD3, CD4, CD14, CD16, CD20, and CD56 antibodies and cells were sorted as CD4 and monocytes.otal RNA was extracted from sorted CD4 T cells and monocytes using the Quick RNA Microprep kit (Zymo research CA, USA) according to the manufacturer’s instructions. RNA concentration and quality were assessed using a Qubit fluorometer (Life Technologies, USA) and TapeStation 2200 system (Agilent Technologies, USA).
Libraries were prepared using the Ovation Solo RNA sequence system (NuGen Technology, CA USA) following manufactures protocol and RNA sequencing was performed using the Illumina MiSeq 2x150 bp paired-end sequencing platform.

treatment_protocol: Infants peripheral blood samples was collected at the time of BCG vaccination and 2 to 13 (average: 7.8 weeks±2.9 weeks) post-BCG vaccination when the infants returned for routine pediatric visits.

value: Monocytes

value: Pre BCG vaccination


title: TBI054_2VST_MONO

description:
Library name: TBI054_2VST_MONO
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0

value: Post BCG vaccination


title: SH-SY5Y TDP-43 knockdown with cycloheximide treatment - TDP-43 control no cycloheximide - 2

description:
Library name: SHSY5Y_CTRL_CTRL_2
SH-SY5Y cells were transduced with a SmartVector lentivirus (V3IHSHEG_6494503) containing a doxycycline-inducible shRNA cassette for TDP-43. Transduced cells were selected with puromycin (1 μg/ml) for one week, before being plated as single cells and expanded to obtain a clonal population. Cells were grown in DMEM/F12 + Glutamax (Thermo) supplemented with 10% FBS (Thermo) and 1% PenStrep (Thermo). For induction of shRNA against TDP-43, cells were treated with 25 ng/ml doxycyline hyclate (Sigma). After 10 days, cells were treated  either with 100 µM cycloheximide (CHX) or DMSO (Pereverzev et al., 2015) for 6 h before isolating the RNA. Overall, 4 conditions were generated: Control for TDP-43 knockdown and DMSO (control/control), Control for TDP-43 knockdown and CHX-treated (control/CHX), Positive for TDP-43 knockdown and DMSO (TDP43/control) and Positive for TDP-43 knockdown and CHX-treated (TDP43/CHX). RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s protocol, including the on-column DNA digestion step.  RNA concentrations were measured by Nanodrop and 1,000 ng of RNA was used for reverse transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x100bp, > 40 million reads per sample).


title: TBI042_2VST_MONO

description:
Library name: TBI042_2VST_MONO
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: TBI042_1VST_MONO

description:
Library name: TBI042_1VST_MONO
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: PN0456_0011

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

country: Italy

institute: Hospital San Raffaele

description: Library name: PN0456_0011_S38

data_processing:
Reads have been trimmed with Cutadapt for adapter sequences and quality and Aligned to the reference genome with STAR
Bam files were counted against the Genecode V31 human GTF annoation of genes (exon and gene_name) using featureCount
Assembly: hg38
Supplementary files format and content: raw count matrices from featureCount with multimapping fractional counts

source_name: umbilical cord blood

growth_protocol: Endothelial colony forming cells (ECFCs) were isolated from umbilical cord blood of full-term pregnancies. Cord-blood mononuclear cells were extracted by density gradient centrifugation and plated on collagen-coated plates (Corning) in EGM-2 medium (Lonza) supplemented with 10% fetal bovine serum (FBS). Plates were cultured in 37oC incubator with 5% CO2. ECFC colonies appeared after 2-3 weeks in culture with cobblestone morphology and immunophenotype confirmed by flow cytometry.

extract_protocol:
Total RNA was isolated using the Maxwell RSC simplyRNA Cells Kit (Promega) and a Maxwell RSC instrument (Promega) following the manufacturer’s instructions. RNA quantity and purity were assessed using the Nanodrop (Thermo Fisher Scientific)and the quality was assessed using the Fragment Analyzer (Agilent Technologies).
Libraries were prepared using KAPA RNA HyperPrep Kit with Poly A enrichment (Roche). Samples were sequenced on a NextSeq 2000 instrument (Illumina) to yield at least 40 million reads per sample, read length 2x50bp PE.

treatment_protocol: ECFCs were transfected with 10nM Silencer select PROCR SiRNA or Scrambled SiRNA control (Thermo Fisher Scientific) at 70% confluency using Lipofectamine RNAiMAX in EGM-2 without antibiotics, for 16 hours. RNA was extracted 48 hrs after transfection.

value: umbilical cord blood

tag: replicate

tag: clone

value: Scrambled SiRNA control


title: TBI038_2VST_MONO

description:
Library name: TBI038_2VST_MONO
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: TBI036_2VST_MONO

description:
Library name: TBI036_2VST_MONO
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: SH-SY5Y TDP-43 knockdown with cycloheximide treatment - TDP-43 knockdown no cycloheximide - 4

description:
Library name: SHSY5Y_DOX_CTRL_4
SH-SY5Y cells were transduced with a SmartVector lentivirus (V3IHSHEG_6494503) containing a doxycycline-inducible shRNA cassette for TDP-43. Transduced cells were selected with puromycin (1 μg/ml) for one week, before being plated as single cells and expanded to obtain a clonal population. Cells were grown in DMEM/F12 + Glutamax (Thermo) supplemented with 10% FBS (Thermo) and 1% PenStrep (Thermo). For induction of shRNA against TDP-43, cells were treated with 25 ng/ml doxycyline hyclate (Sigma). After 10 days, cells were treated  either with 100 µM cycloheximide (CHX) or DMSO (Pereverzev et al., 2015) for 6 h before isolating the RNA. Overall, 4 conditions were generated: Control for TDP-43 knockdown and DMSO (control/control), Control for TDP-43 knockdown and CHX-treated (control/CHX), Positive for TDP-43 knockdown and DMSO (TDP43/control) and Positive for TDP-43 knockdown and CHX-treated (TDP43/CHX). RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s protocol, including the on-column DNA digestion step.  RNA concentrations were measured by Nanodrop and 1,000 ng of RNA was used for reverse transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x100bp, > 40 million reads per sample).


title: TBI032_1VST_MONO

description:
Library name: TBI032_1VST_MONO
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: PN0456_0010

description: Library name: PN0456_0010_S37

value: Endothelial colony forming cells (ECFCs)

value: PROCR SiRNA


title: PN0456_0009

description: Library name: PN0456_0009_S36


title: TBI004_2VST_MONO

description:
Library name: TBI004_2VST_MONO
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: TBI025_2VST_MONO

description:
Library name: TBI025_2VST_MONO
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: SH-SY5Y TDP-43 knockdown - doxycycline 75 ng/ml - 2

description:
Library name: SHSY5Y_DOX_075_2
SH-SY5Y cells were transduced with a SmartVector lentivirus (V3IHSHEG_6494503) containing a doxycycline-inducible shRNA cassette for TDP-43. Transduced cells were selected with puromycin (1 μg/ml) for one week, before being plated as single cells and expanded to obtain a clonal population. Cells were grown in DMEM/F12 + Glutamax (Thermo) supplemented with 10% FBS (Thermo) and 1% PenStrep (Thermo). For induction of shRNA against TDP-43, cells were treated with the following amounts of doxycycline hyclate (Sigma) and collected after 10 days: 12.5 ng/ml, 18.75 ng/ml, 21 ng/ml, 25 ng/ml, and 75 ng/ml. RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s protocol, including the on-column DNA digestion step.  RNA concentrations were measured by Nanodrop and 1,000 ng of RNA was used for reverse transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x100bp, > 40 million reads per sample).

extract_protocol:
RNA  was  extracted using  the  RNeasy  mini  kit  (Qiagen)  following  the  manufacturer’s  protocol,  including  the on-column  DNA  digestion  step.  RNA  concentrations  were  measured  by  Nanodrop  and  1,000  ng of  RNA  was  used  for  reverse  transcription.
Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (SH-SY5Y = 2x100bp, > 40 million reads per sample).


title: SH-SY5Y TDP-43 knockdown - doxycycline 75 ng/ml - 3

description:
Library name: SHSY5Y_DOX_075_3
SH-SY5Y cells were transduced with a SmartVector lentivirus (V3IHSHEG_6494503) containing a doxycycline-inducible shRNA cassette for TDP-43. Transduced cells were selected with puromycin (1 μg/ml) for one week, before being plated as single cells and expanded to obtain a clonal population. Cells were grown in DMEM/F12 + Glutamax (Thermo) supplemented with 10% FBS (Thermo) and 1% PenStrep (Thermo). For induction of shRNA against TDP-43, cells were treated with the following amounts of doxycycline hyclate (Sigma) and collected after 10 days: 12.5 ng/ml, 18.75 ng/ml, 21 ng/ml, 25 ng/ml, and 75 ng/ml. RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s protocol, including the on-column DNA digestion step.  RNA concentrations were measured by Nanodrop and 1,000 ng of RNA was used for reverse transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x100bp, > 40 million reads per sample).


title: PN0456_0008

description: Library name: PN0456_0008_S35


title: SH-SY5Y TDP-43 knockdown - doxycycline 75 ng/ml - 1

description:
Library name: SHSY5Y_DOX_075_1
SH-SY5Y cells were transduced with a SmartVector lentivirus (V3IHSHEG_6494503) containing a doxycycline-inducible shRNA cassette for TDP-43. Transduced cells were selected with puromycin (1 μg/ml) for one week, before being plated as single cells and expanded to obtain a clonal population. Cells were grown in DMEM/F12 + Glutamax (Thermo) supplemented with 10% FBS (Thermo) and 1% PenStrep (Thermo). For induction of shRNA against TDP-43, cells were treated with the following amounts of doxycycline hyclate (Sigma) and collected after 10 days: 12.5 ng/ml, 18.75 ng/ml, 21 ng/ml, 25 ng/ml, and 75 ng/ml. RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s protocol, including the on-column DNA digestion step.  RNA concentrations were measured by Nanodrop and 1,000 ng of RNA was used for reverse transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x100bp, > 40 million reads per sample).


title: TBI017_1VST_MONO

description:
Library name: TBI017_1VST_MONO
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: PN0456_0007

description: Library name: PN0456_0007_S34


title: TBI056_2VST_CD4

description:
Library name: TBI056_2VST_CD4
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: TBI058_2VST_CD4

description:
Library name: TBI058_2VST_CD4
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: TBI058_1VST_CD4

description:
Library name: TBI058_1VST_CD4
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: i3Neuron TDP-43 knockdown (30 days) - Control 1

description:
Library name: CTRL-1
Human iPS cells used in this study were engineered from WTC11 line to express mouse or human neurogenin-2 under a doxycycline-inducible promoter (Fernandopulle et al., Current Protocols in Cell Biology, 2018; Wang et al., Stem Cell Reports, 2017) and an enzymatically dead Cas9 (+/- CAG-dCas9-BFP-KRAB) at safe-harbour loci (Tian et al., Neuron, 2019). CRISPRi  knockdown of TDP-43 in iPSCs was achieved  using  sgRNA  targeting  the  transcription  start  site  of  TARDBP (GGGAAGTCAGCCGTGAGACC) or a non-targeting control (GTCCACCCTTATCTAGGCTA), delivered by lentiviral transduction. i3Neurons  were  induced  as previously  described (Fernandopulle et al., Current Protocols in Cell Biology, 2018)  with  the  addition  of  SMAD  and  WNT  inhibitors  (Nehme et al., Cell Reports, 2018)(SB431542  10  µM; LDN-193189  100  nM;  XAV939  2  µM  all  from  Cambridge  Biosciences). After  induction,  cells were cultured in BrainPhys Media (StemCell  Technologies) with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1x N2 supplement (Thermo  Fisher), 1  x B27 supplement (Thermo Fisher), 200 nM Ascorbic Acid (Sigma), 1 mM dibutyryl cyclic-AMP (Sigma) and 1 µg/ml Laminin (Thermo  Fisher) as previously  described (Bardy et al., PNAS, 2015) and harvested 30 days after differentiation. Strand-specific, poly(A) enriched sequencing libraries dataset were prepared using the Kapa mRNA Hyper Prep kit. 100ng total RNA was used as input material for poly(A)+ mRNA capture. Fragmentation was performed for 6 minutes at 85°C to obtain a target fragment size of 300-400bp, and 13 cycles of PCR amplification were performed. The resulting libraries were sequenced 2x150bp on the Illumina NextSeq2000 machine.

value: iPSC-derived cortical neuron


title: TBI056_1VST_CD4

description:
Library name: TBI056_1VST_CD4
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: SH-SY5Y TDP-43 knockdown - doxycycline 0 ng/ml - 3

description:
Library name: SHSY5Y_DOX_0_3
SH-SY5Y cells were transduced with a SmartVector lentivirus (V3IHSHEG_6494503) containing a doxycycline-inducible shRNA cassette for TDP-43. Transduced cells were selected with puromycin (1 μg/ml) for one week, before being plated as single cells and expanded to obtain a clonal population. Cells were grown in DMEM/F12 + Glutamax (Thermo) supplemented with 10% FBS (Thermo) and 1% PenStrep (Thermo). For induction of shRNA against TDP-43, cells were treated with the following amounts of doxycycline hyclate (Sigma) and collected after 10 days: 12.5 ng/ml, 18.75 ng/ml, 21 ng/ml, 25 ng/ml, and 75 ng/ml. RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s protocol, including the on-column DNA digestion step.  RNA concentrations were measured by Nanodrop and 1,000 ng of RNA was used for reverse transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x100bp, > 40 million reads per sample).


title: PN0456_0006

description: Library name: PN0456_0006_S33


title: TBI054_2VST_CD4

description:
Library name: TBI054_2VST_CD4
Post BCG vaccinated sequencing files vs Pre BCG vaccinated files  were processed  using the CLC genomics workbench 22.0


title: PN0456_0012

description: Library name: PN0456_0012_S39