title: TUM_108

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_108


title: TUM_44

status: Public on Mar 07 2025

type: RNA

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

description: Gene expression data from bladder tumor

hyb_protocol: Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix, corresponding to the U133plus 2.0 arrays

scan_protocol: Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.

data_processing: Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: HGU133Plus2_Hs_ENTREZG,  Brainarray Custom CDF EntrezG version 22,

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Bladder tumor samples TUM_44

label_protocol: 100ng of total RNA were amplified to produced biotinylated complementary RNAs, as recommended by Affymetrix.

extract_protocol: Tumor RNA was extracted using Qiazol (Qiagen, Courtaboeuf, France) according to the manufacturer instructions and purified using miRNeasy Mini kit (Qiagen).

treatment_protocol: Bladder tumors were directly snap frozen in liquid nitrogen after resection and stored at -80°C. DNA, RNA and proteins were obtained following a triple extraction protocol

tag: disease state

value: bladder cancer


title: Con-818

type: SRA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

country: China

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Library name: Con-818

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.
Supplementary files format and content: Excel file includes FPM values for each Sample.

organism: Mus musculus

source_name: aorta

extract_protocol:
The isolated small intestine are quickly put into RNA later (Invitrogen, Waltham, Massachusetts, USA) and stored at low temperature. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from islets according to the manufacturer's protocol. The amount of total RNA was measured with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA), and the quality was evaluated by 1% agarose gel electrophoresis, and stained with 4S Red Plus nucleic acid stain (Sango, Shanghai, China).
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit.

tag: tissue

value: aorta

tag: genotype

value: WT

tag: treatment

value: saline


title: TUM_40

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_40


title: SJBALL030040_D1 scRNA-seq

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

country: USA

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

library_source: transcriptomic single cell

data_processing:
Single-cell RNA-seq data were aligned and quantified using the Cell Ranger (v5.0.1) pipeline against the human genome.
Assembly: hg38
Supplementary files format and content: Standard cellranger output format including Market Exchange format for  feature-barcode matrix and tab-separated value (tsv) format for barcode and feature sequences

source_name: primary sample

extract_protocol:
Chromium scRNA-seq Next GEM Single Cell 5' v2 (10X Genomics)
TruSeq Read 1 and TruSeq Read 2; Sequencing Read: Read 1: 26 cycles, i7 Index: 10 cycles, i5 Index: 10 cycles, Read 2: 90 cycles

tag: cell type

value: primary leukemia sample

value: untreated


title: SJBALL030059_D1 scRNA-seq


title: Con-810

description: Library name: Con-810


title: TUM_38

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_38


title: SJBALL030036_D1 scRNA-seq


title: BV-2 cells, sh s2

city: XuZhou

first: xinxing

last: huang

state: JiangSu

address: 209 Tongshan Road

institute: university

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.txt:  sh_s2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Assembly: mm8
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: cell line

growth_protocol: Mouse BV2 microglia cells were cultured in Dulbecco’s Modified Eagle’s Medium High glucose in the 5% CO2, 37 ℃ incubator, which contained fetal bovine serum  and penicillin/streptomycin .

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: BV2 cells were treated with LPS (100 ng/mL) for 24h.

value: cell line

tag: cell line

value: Microglia cells

value: SIX2 knockdown

value: LPS


title: SJBALL022052_D1 scRNA-seq


title: Con-811

description: Library name: Con-811


title: Con-824

description: Library name: Con-824


title: TUM_37

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_37


title: TUM_33

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_33


title: TUM_30

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_30


title: BV-2 cells, sh s1

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.txt:  sh_s1


title: SJBALL022035_D1 scRNA-seq


title: Con-820

description: Library name: Con-820


title: SJBALL021973_D1 scRNA-seq


title: TUM_23

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_23


title: TUM_36

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_36


title: BV-2 cells, sh c2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.txt:  sh_c2


title: TUM_7

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_7


title: SJBALL021947_D1 scRNA-seq


title: NC-4, hepatic tissue

city: Shanghai

first: Li

last: Cheng

state: Shanghai

address: 500 Quxi Road, Shanghai 200011

department: Department of Rehabilitation Medicine

institute: The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
The raw paired-end fastq reads underwent filtering by TrimGalore to eliminate adapters and low-quality bases, which was accomplished through the utilization of the Cutadapt tool.
The resulting clean reads were then aligned to the genome using HISAT2, followed by reference-guided transcriptome assembly and gene expression quantification utilizing StringTie.
Assembly: Rnor_6
Supplementary files format and content: tab-delimited text files include gene_count values, gene_tpm value for each Sample

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424)
High-quality RNA samples were used to construct a sequencing library.

value: liver

tag: Sex

value: male

value: normal control


title: TUM_25

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_25


title: SJBALL022020_D1 scRNA-seq


title: TUM_14

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_14


title: SJBALL021901_D1 scRNA-seq


title: TUM_17

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_17


title: J1.1 cells treated with Birinapant 20A

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
nf-core/rna seq pipeline used to align data
DESeq2 used to perform fold change calculation based on salmon read counts
Assembly: GRCh38, GENCODE.v46
Supplementary files format and content: salmon.merged.gene_counts.tsv. Tab delimited table of salmon read counts form all samples
Supplementary files format and content: MG1_vs_UT.txt ,tab delimited table of DESeq fold change between conditions
Supplementary files format and content: B1_vs_UT.txt,tab delimited table of DESeq fold change between conditions
Supplementary files format and content: BMG1_vs_UT.txt,tab delimited table of DESeq fold change between conditions

source_name: lymphoblastic leukemia

growth_protocol: Cells were grown in serum and L-glutamine containing RPMI at 37C

extract_protocol:
Cells were lysed and RNA was extracted using Qiagen RNeasy mini kit (cat#74104) RNA sample quality assessment was performed with the Fragment Analyzer (Agilent) and concentration measured with the Qubit 3.0 (Thermo). Sequencing was performed with the Nextseq 2000 P3 100 cycle flow cell (Illumina).
NGS libraries were prepared with the Stranded mRNA library prep kit (Illumina) using 500 ng of RNA input.

treatment_protocol: Cell conditions are untreated, infected with MG1_eGFP, infected with MG1_eGFP and treated with Birinapant, and treated with Birinipant only.

value: lymphoblastic leukemia

value: Childhood T acute lymphoblastic leukemia cells containing one copy of HIV

value: J1.1 cells were plated at density 1x106 cells/mL and treated with 1 µM Birinapant for 48h


title: NC-3, hepatic tissue


title: BV-2 cells, sh c1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.txt:  sh_c1


title: TUM_8

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_8


title: musculus_Adult_optic_musculus_Age_optic_musculus_Age_PLX_optic_rep2

city: Munich

first: Ruoqing

last: Feng

address: Feodor-Lynen-Strasse 17

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description:
Library name: M2
multiplexed,Chromium Fixed RNA Profiling Reagent Kits

library_source: other

data_processing:
The reads were aligned to the University of California, Santa Cruz mouse mm10 reference genome and data were demultiplexed using the CellRanger software v.7.1.0; with the cellranger multi model (more detal can be found at https://www.10xgenomics.com/cn/support/software/cell-ranger/latest/resources/cr-command-line-arguments). All parameter were set as defalt. The 2 libraries are both multiplexed with, BC001:Adult; BC002:Aged; BC003:Aged PLX treatment.
Assembly: University of California, Santa Cruz mouse mm10
Supplementary files format and content: Sparse Matrix in h5

molecule: other

source_name: Optic nerve

extract_protocol:
Fixed single cells were sorted and counted before probe hybridization with barcodes for multiplexing, pooling, washing, and loading into the Chromium X (10x Genomics).
Complementary DNA libraries ready for sequencing on Illumina platforms were generated using the Chromium Single Cell 3′ Library & Gel Bead Kit v3.1 (10x Genomics) or the Chromium Fixed RNA Kit (10x Genomics) according to the detailed protocol provided by the manufacturer. Libraries were quantified by Qubit 3.0 Fluorometer (Thermo Fisher Scientific) and quality was checked using a 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent Technologies). Libraries were pooled and sequenced with a NovaSeq 6000 platform (S1 Cartridge; Illumina) in paired-end mode.

treatment_protocol: PLX5622 (provided by Plexxikon Inc., Berkeley, CA, USA) was prepared as a 300 ppm drug chow to dose ~ 54 mg PLX5622/kg body weight when given ad libitum. This was based on our previous long-term treatment approaches in which we observed efficient microglia depletion without obvious neurological side effects67,68. Control mice received normal chow without the pharmacological inhibitor. Mice were treated for 6, 12, or 24 months with daily monitoring concerning certain burden criteria and phenotypic abnormalities. The treatment started before obvious aging-related pathology in mice at 18, 12, or 0 months of age (by post-partum treatment of lactating mothers and continued post-weaning treatment of pups).

value: Optic nerve

value: Wild type

value: PLX treatment


title: model-4, hepatic tissue

value: adjuvant arthritic (AA)


title: J1.1 cells treated with Birinapant 15A


title: NC-2, hepatic tissue


title: model-1, hepatic tissue


title: SJBALL021968_D1 scRNA-seq


title: J1.1 cells treated with Birinapant S1


title: SJBALL006_D scRNA-seq


title: GCK-4, hepatic tissue

value: GCK


title: J1.1 cells treated infected with MG1_eGFP and treated with the SMAC mimetic Birinapant 20A

value: J1.1 cells were plated at density 1x106 cells/mL and infected with MG1_eGFP at 1000 pfu and treated with 1µM Birinapant for 48h.


title: J1.1 cells treated infected with MG1_eGFP and treated with the SMAC mimetic Birinapant 15A


title: SJBALL004097_D2 scRNA-seq

value: primary leukemia sample

value: untreated


title: J1.1 cells treated infected with MG1_eGFP S1

value: J1.1 cells were plated at density 1x106 cells/mL and infected with MG1_eGFP at 1000 pfu for 48h.


title: model-3, hepatic tissue


title: GCK-3, hepatic tissue


title: J1.1 cells 20A


title: J1.1 cells treated infected with MG1_eGFP and treated with the SMAC mimetic Birinapant S1


title: SJALL040137_R1 scRNA-seq


title: model-2, hepatic tissue


title: J1.1 cells 15A


title: SJBALL014876_D1 scRNA-seq


title: J1.1 cells treated infected with MG1_eGFP 20A


title: GCK-1, hepatic tissue


title: SJBALL006_R scRNA-seq


title: SJBALL021964_D1 scRNA-seq


title: J1.1 cells S1


title: J1.1 cells treated infected with MG1_eGFP 15A


title: musculus_Adult_optic_musculus_Age_optic_musculus_Age_PLX_optic_rep1

description:
Library name: M1
multiplexed,Chromium Fixed RNA Profiling Reagent Kits


title: Atg16_flox_2

city: St. Louis

first: Christina

last: Stallings

state: MO

address: 425 South Euclid ave

institute: Washington University in Saint Louis

data_processing:
demultiplexing was performed using fastq-multx
Reads were aligned to Ensemble release 76 primary assembly with STAR 2.5.1a
Counts were obtained using Subread:featureCount and Salmon 0.8.2
Sequencing QC was performed using RSeQC 2.6.2
Assembly: GRCm38.p3
Supplementary files format and content: raw-delimeted text file includes raw counts for each sample

source_name: Lung

extract_protocol:
RNA was extracted from neutrophils using TRIzol Reagent (Invitrogen).
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovoSeq

value: Lung

value: neutrophils


title: Atg16_flox_1


title: DLPFC 1-888

city: Tampa

first: Jinying

last: Zhao

state: FL

address: 3650 Spectrum Blvd

institute: University of South Florida

description:
Library name: brain1-brain888
The raw data are being made available for controlled access in Synapse.

library_source: genomic

data_processing:
Raw sequencing reads were trimmed by Trimmomatic v0.39 to remove adapter sequences and poor-quality reads. High-quality reads were mapped to the reference human genome GRCh38 by Bowtie2-2.3.5.1 with uniquely mapped reads retained for the following analyses. PCR duplicates were removed by Picard v2.21.2. We used MACS2 (v2.2.7.1) to identify DhMRs with default parameters, except for enabling the --broad option to call broad peaks at a threshold of q-value<0.01. Additionally, twelve input samples were combined and used as control samples during peak calling for all samples. After peak calling, all peaks with at least one base pair (bp) overlapping across all samples were merged using DiffBind v3.0 (https://bioconductor.org/packages/devel/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf). The read counts were then re-calculated for each merged peak. Consensus regions were normalized by trimmed mean of M-values (TMM) implemented in the edgeR Bioconductor package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: hMe-Seal

molecule: genomic DNA

source_name: DLPFC bulk tissue

extract_protocol:
Genomic DNA from ~100 mg sections of frozen dorsolateral prefrontal cortex (DLPFC) was isolated by homogenizing the samples in 600 μl digestion buffer (100 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl), Proteinase K (Thermo Fisher, cat# EO0491) treatment at 55°C for overnight. Following digestion, 600 μl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1 Saturated with 10 mM Tris, pH 8.0, 1 mM EDTA) (Sigma-Aldrich, cat# P-3803) was added and mixed thoroughly prior to centrifugation at 16,000g for 10 min. PicoGreen was used to quantitate the DNA.
5hmC enrichment was performed according to the previously described 5hmC-specific chemical labeling and affinity purification protocol. Briefly, DNA libraries were prepared using 2 μg of captured DNA or input DNA and performed following the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® manufacturers protocol. Prior to sequencing, the quality of prepared libraries was checked using Bioanalyzer and TapeStation. Sequencing was performed on the HiseqX 2 x150 platform.

value: DLPFC bulk tissue


title: GCK-2, hepatic tissue

value: liver

value: male


title: SJALL040103_D1 scRNA-seq

source_name: primary sample


title: DEX-2, hepatic tissue

value: DEX


title: SJALL040137_D1 scRNA-seq


title: Atg16_cre_4


title: Atg16_cre_3


title: Atg5_flox_2


title: DEX-4, hepatic tissue


title: NC-1, hepatic tissue

value: normal control


title: DLPFC 879-1050

description:
Library name: brain879-brain1050
The raw data are being made available for controlled access in Synapse.


title: DEX-1, hepatic tissue


title: SJALL040119_D1 scRNA-seq


title: Atg16_cre_2


title: Atg5_cre_3


title: SJALL040100_D1 scRNA-seq


city: London

first: Jake

last: Cornwall-Scoones

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

description: Library name: NeMECiS_D6neural_progenitors_500nMSAG_Rep2

data_processing:
A white-list of all 15,625 possible barcode concatemers was generated using a custom script. These were appended with left and right adaptor sequences to establish amplicons.fa, containing sequences each of length 163bp, labelled with the corresponding composition and ordering of CRE fragments. These have a generic form:    [TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG][AGCA][NNNNNNNN][GATT][NNNNNNNN][AGCA][NNNNNNNN][GATT][GATTAATAAAGGAAATTTATTTCATTGCAATAGTGTGTTGGAATTTGTGTCTCTCA][CTGTCTCTTATACACATCTCCGAGCCCACGAGAC]  [Nextera Rd1][Golden Gate overhang][8bp-BC sequence][Golden Gate overhang][8bp-BC sequence] [Golden Gate overhang][8bp-BC sequence][Golden Gate overhang][polyA terminator sequence ][Nextera Rd2]  Bowtie 2 was used for barcode calling. Index files were generated using the command: bowtie2-build amplicons.fa Global alignment of barcode concatemers for each fastq file from the NextSeq 500 demultiplexed output was achieved by running the following command, trimming alignment to exclude Nextera adaptors:  bowtie2 --threads 32 --trim-to 3:96 -x amplicons -1 fastq_file_read1.fastq -2 fastq_file_read2.fastq From the alignments recorded in the .sam file output, a custom python script was used to generate a count-matrix for each barcode in each sample. Here, reads by barcode were counted that had a perfect match (CIGAR output of 96M), and successfully aligned to a member of the white-list.
A Bayesian inference framework was used to calculate the (distribution) of (log) ZsGreen fluorescence for each synCRE by condition and replicate. In brief this performs the following steps: - Assume each synCRE produces a log fluorescence profile that is normally distributed - Pool of synCREs are parameterised by their relative densities in the pool, and the mean and variance of their log ZsGreen levels. - Sort bins are calibrated using measured flow distributions of sorted pools. - Finite number effects are simulated through sequential binomial sampling: (1) finite number of sorted cells; (2) finite number of reads. - Posterior probability distribution of each synCRE’s mean, variance and density given observed read-counts in each of the sorted bins and the unsorted population is inferred using the NUTS sampler (STAN)
https://github.com/jakesorel/NeMECiS
The GEO submission relates to folders "inference<https://github.com/jakesorel/NeMECiS/tree/main/inference>" and "alignment<https://github.com/jakesorel/NeMECiS/tree/main/alignment>"
Assembly: FASTA file is on series record.
Supplementary files format and content: Processed data csv file for plasmid library has the following structure. Rows are unique synCREs.  'Pos1', 'Pos2', 'Pos3' = fragment identities in positions 1,2,3 (from furthest to nearest the promoter) “Counts” = number of reads aligned by synCRE 'fragment_combination' = Combination of fragments in the synCRE (5’-3’) 'barcode_combination’= Combination of barcodes in the synCRE (5’-3’) BC_concatemer_seq' = Barcode concatemer aligned sequence 'BC1_seq' = Breakdown thereof for barcode 1 'synCRE_seq' = Full 608bp synCRE sequence 'Frag1_seq’ = Breakdown thereof for Fragment 1
Supplementary files format and content: Processed data csv files for neural progenitors has the following structure. Rows are unique synCREs.  'Pos1', 'Pos2', 'Pos3' = fragment identities in positions 1,2,3 (from furthest to nearest the promoter)  'estimated_mean_log_ZsGreen' = Bayesian inference of max-likelihood mean logZsGreen 'estimated_mean_log_ZsGreen_se' = Bayesian inference of standard error thereof 'passes_QC' = Passes quality control in this sample  'passes_QC_all_samples' = Passes quality control across all samples 'estimated_proportion_of_pool' = Bayesian estimate of max-likelihood relative density of this synCRE in the unsorted pool 'estimated_proportion_of_pool_se' = Standard error thereof 'estimated_std_log_ZsGreen' = Bayesian estimate of max-likelihood log ZsGreen standard deviation 'estimated_std_log_ZsGreen_se' = Standard error thereof  'Bin1_Counts_L001' = Read counts in Bin 1 and NextSeq sequencing lane L001 'Bin1_Counts' = Read counts in Bin 1, aggregated over sequencing lanes 'fragment_combination' = Combination of fragments in the synCRE (5’-3’) 'barcode_combination’= Combination of barcodes in the synCRE (5’-3’) BC_concatemer_seq' = Barcode concatemer aligned sequence 'BC1_seq' = Breakdown thereof for barcode 1 'synCRE_seq' = Full 608bp synCRE sequence 'Frag1_seq’ = Breakdown thereof for Fragment 1

source_name: neural progenitor differentiation

growth_protocol: Plasmid library: Cloning product was transformed using 25uL Endura Electrocompetent Cells (60242-1) and grown at 28ºC (170rpm) in 1L L-Broth supplemented with Carbenicillin.  Neural progenitors: All experiments were carried out using the HM1 mouse embryonic stem cell (mESC) line, maintained at 37°C with 5% CO2. mESCs were maintained in ESGRO Complete PLUS Clonal Grade Medium (Merck Millipore, Cat No. SF001-500P) supplemented with 1% Penicillin/Streptomycin (Gibco, Cat No. 15140122) on CellBIND tissue-culture plates (Corning, Cat No. 3335) coated with 0.15% gelatin (Gibco, Cat no. G1393-100ML). Infected, selected cells (see below) were expanded for one passage in ESGRO and Puromycin Dihydrochloride. 200mm tissue culture plates were coated with 1:100 Vitronectin diluted in DMEM-F12 (-/-) (Gibco, Cat No. 21331-020) for 1 hour. Per replicate, a total of  6x10^7 cells cells were plated in N2B27 supplemented with bFGF as above. After 48 hours, media was changed into N2B27 supplemented with bFGF and CHIR99021 as above. After a further 20 hours, cells were dissociated with StemPro Accutase (Gibco, Cat No. A1110501), centrifuged, and re-plated at a 1:1 ratio in N2B27 supplemented with 100 nM RA (Sigma, Cat. No. R2625, additionally supplementing the media for half of the cells with 500 nM SAG (Merck, Cat. No. 566660-5mg), onto plates coated with 1:100 GelTrex diluted in DMEM-F12 (-/-) (Gibco, Cat No. 21331-020). Media was changed daily. After 72 hours, cells were dissociated with StemPro Accutase, centrifuged and resuspended in 0.5% BSA (Sigma-Aldrich, Cat No. A7979-50ML) in PBS (Gibco, Cat. No. 14190-094). 30% of each sample was immediately pelletted and frozen, and the remaining cells were flow sorted, as described below.  24 hours before flow sorting, 10mL polypropylene tubes were incubated with 100% Fetal Bovine Serum. Prior to sorting, samples were supplemented with 10 ng/ml DAPI (Invitrogen, Cat No. D1306). Samples were run on MoFlo XDP and BD InFlux. Sorted events were gated on live singlets (FSC-A vs SSC-A; SSC-A vs SSC-H; FSC-A vs DAPI). Four bins of ZsGreen intensity were established for each sample (two replicates, each for 0 nM and 500 nM SAG), demarcating the following percentile bins, following an optimal binning strategy (de Boer et al., 2020). FBS in polypropylene tubes was decanted and samples were sort according to the above gating strategy. To assess sort quality and calibrate downstream analysis, 10 L of each sorted sample, as well as the unsorted pool, were extracted and run on the BD LSRFortessa Cell Analyzer.

extract_protocol:
Plasmid library: 200mL of the OD600=1.0 bacterial culture was extracted using the Qiagen Plasmid Plus Maxi Kit (12963), according to manufacturer’s instructions. Neural progenitors: To extract genomic DNA, sorted cells for the NeMECiS screen were pelleted in 1.5mL DNA LoBind microfuge tubes (Eppendorf, Cat No. Z666548) by centrifugation for 10 minutes at 500g. Genomic DNA was extracted for sorted and unsorted pellets using a Quick-DNA Miniprep Plus Kit according to the manufacturer’s instructions (Zymo Research, Cat No. D4069), dividing each sorted sample into six columns each. Each column was eluted in 75 L of the supplied elution buffer (10 mM Tris-HCl, pH 8.5, 0.1 mM EDTA) pre-warmed to 60ºC, into 1.5mL DNA LoBind microfuge tubes, pooling the samples of the same origin to bring the total eluted gDNA to 450uL.
Barcode concatemers were amplified by PCR using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, Cat. No M0541L) by combining on ice: 450 L gDNA, 500 L 2X master mix, 5 L each of 100 M Nextera-adaptor primers (indexing each sample, see below), and 40 L nuclease-free water. Amplification was carried out under the following program: 5 minutes at 72°C, 30 seconds at 98°C, followed by 17 cycles of 30 seconds at 98°C, 30 seconds at 63 °C and 60 seconds at 72°C, and subsequently 5 minutes at 72°C. At this step, all PCR products were pooled. The pooled amplicon DNA was then cleaned up using 1.8x v/v of AMPureXP beads (Beckman Coulter, Cat. No. A63882) and eluted in 50 L EB buffer (10 mM Tris-Cl, pH 8.5). Library concentration was determined using the KAPA Library Quanitification Complete Kit Universal (Roche, Cat No. 07960140001) according to manufacturer’s instructions, using the QuantStudio 12K Flex Real-Time PCR System for qPCR (Applied Biosystems, Cat No. 4471087). 50% of the amplified sequence was further amplified using NEBNext High-Fidelity 2X PCR Master Mix and P5 (AATGATACGGCGACCACCGA) and P7 primers (CAAGCAGAAGACGGCATACGAGAT) using the same programme as above, then re-quantified as above to establish a concentration in excess of 1nM. Size spectra were examined with a Bioanalyzer using the DNA High Sensitivity DNA Kit (Agilent, Part No. 5067-4626) to confirm library quality. The plasmid library was sequenced using the Illumina MiniSeq Sequencer on a ‘High Output’ run using the MiniSeq High Output Reagent Kit (300-cycles) (Illumina, Cat No. FC-420-1003) according to the manufacturer’s instructions. The neural progenitor library was sequenced using the Illumina NextSeq 500 Sequencer on a ‘High Output’ run using the NextSeq 500/550 High Output Kit v2.5 (300 Cycles) (Illumina, Cat No. 20024908) according to the manufacturer’s instructions.  Sequence demultiplexing was performed with the built-in software by supplying the corresponding indexing sequences for each sample.

treatment_protocol: In duplicate, 10^7 mESCs were infected with the NeMECiS lentivirus library in ESGRO at MOI<1, maintained in CellBIND T175 flasks (Corning, CatNo. 3292). After 48 hours, media was changed into ESGRO supplemented with 1ug/mL Puromycin Dihydrochloride (Gibco, Cat No. 12122530).

value: neural progenitor differentiation


title: DEX-3, hepatic tissue


description: Library name: NeMECiS_D6neural_progenitors_500nMSAG_Rep1


description: Library name: NeMECiS_D6neural_progenitors_0nMSAG_Rep1


description: Library name: NeMECiS_D6neural_progenitors_0nMSAG_Rep2


title: Atg5_cre_2


title: Atg16_cre_1


title: SJALL040066_D1 scRNA-seq


title: adr-2(-); ADR-1 dsRBD1 neural cells biol rep 1

city: Bloomington

first: Ananya

last: Mahapatra

address: 316 E University St

institute: Indiana University, Bloomington

description: Library name: Sample 4_GSF3747

data_processing:
Reads were aligned to C. elegans reference genome using STAR (v.2.7.8a)
Differential gene expression analysis was performed using Feature counts and DeSeq2.
Assembly: C. elegans WS275
Supplementary files format and content: .csv files include DeSeq2 analysis

organism: Caenorhabditis elegans

source_name: L1 neural cells

growth_protocol: After hatching using bleaching, L1 animals were washed off plates and neural cells were isolated

extract_protocol:
For the neural cell samples, after bleaching, neural cells were isolated from the animals and collected in Trizol (Invitogen) and purified using TURBO Dnase(Ambion) followed by RNeasy extraction kit (Qiagen)
Poly-A selected mRNA library preparation was done using KAPA stranded library preparation kit

value: L1 neural cells

value: Neural cells from worms

tag: strain

value: adr-2(-); ADR-1 dsRBD1

value: Bleaching was performed to collect L1 animals and neural cells were isolated and collected in trizol


title: SJALL040069_D1 scRNA-seq


title: adr-2(-); ADR-1 dsRBD1 neural cells biol rep 3

description: Library name: Sample 6_GSF3747


title: adr-2(-); ADR-1 dsRBD1 neural cells biol rep 2

description: Library name: Sample 5_GSF3747


title: Input_Mettl14KO_NPC

city: Philadelphia

first: Yachen

last: Shen

address: 3400 Civic Center Blvd, Philadelphia, PA 19104

institute: University of Pennsylvania

description:
Library name: Sample10
m6A-seq

data_processing:
*library strategy: m6A-seq
Raw sequencing data from m6A-seq were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina), and adaptors were trimmed using Trimmomatic v0.32 software with MINLEN(Bolger et al., 2014). Alignments were made using STAR v2.5.2a to GENCODE mouse reference genome GRCm38.p6 or the GENCODE human reference genome GRCh38.p13. All m6A modification sites were examined using the BAM file generated from STAR, applying exomePeak2 with criteria of fold change > 2 compared to input and FDR < 0.01).
Assembly: GRCm38.p6
Supplementary files format and content: m6A peak files from exomepeak2

molecule: polyA RNA

source_name: hypothalamic neural progenitor cells

extract_protocol:
Mouse NPCs were isolated from E14.5 Mettl14f/f mouse embryonic hypothalamus using papain solution and cultured in DMEM/F12 containing 20 ng/ml FGF2, 20 ng/ml EGF, 2% B27 without VA, Glutamax, N2 and  Penicillin/Streptomycin on culture dishes precoated with Matrigel matrix (2%). For knocking out Mettl14 from mouse hypothalamic NPCs, NPCs were incubated with culture medium containing lenti-EGFP-Cre or lenti-EGFP and the medium is refreshed after a 24-hour incubation period.After 72 hours, we isolate EGFP-positive cells using flow cytometry at the Penn Core Facility.
Enrichment of polyadenylated RNA from total RNA was performed using Oligo(dT) dynabeads according to the manufacturer’s protocol. The polyadenylated RNA was chemically fragmented into ∼80-nt-long fragments using zinc fragmentation reagent. To purify the RNA, 20 μl MyOne Silane Dynabeads were washed in 100 μl RLT, resuspended in 30 μl RLT, and added to the eluted RNA. 60 μl 100% ethanol was added to the mixture, the mixture attached to the magnet and the supernantant discarded. Following two washes in 100 μl of 70% ethanol, the RNA was eluted from the beads in 16.5 µl water. Optimizing m6A-modified RNA enrichment via the utilization of polyadenylated RNA fragments from 30µg total RNA with EpiMark N6-Methyladenosine Enrichment Kit (NEB) following the manufacturer's protocol. Then the IP samples were used for cDNA library preparation with the NEBNext Ultra II RNA Library Prep Kit. Sequencing library fragment sizes were quantified by bioanalyzer with an average size of ∼400 bp, and concentrations were quantified by qPCR (KAPA). Samples were pooled, loaded at 2.7 pM, and sequenced on a Next-Seq 500 (Illumina).

value: hypothalamic neural progenitor cells

value: Mettl14 Knockout

value: input


title: Atg5_flox_1


title: Input_Control_NPC

description:
Library name: Sample9
m6A-seq

growth_protocol: Mouse NPCs were isolated from E14.5 Mettl14f/f mouse embryonic hypothalamus using papain solution and cultured in DMEM/F12 containing 20 ng/ml FGF2, 20 ng/ml EGF, 2% B27 without VA, Glutamax, N2 and  Penicillin/Streptomycin on culture dishes precoated with Matrigel matrix (2%).

treatment_protocol: For knocking out Mettl14 from mouse hypothalamic NPCs, NPCs were incubated with culture medium containing lenti-EGFP-Cre or lenti-EGFP and the medium is refreshed after a 24-hour incubation period.After 72 hours, we isolate EGFP-positive cells using flow cytometry at the Penn Core Facility.

value: Control


title: adr-2(-) neural cells biol rep 2

description: Library name: Sample 2_GSF3747


title: SJALL040070_D1 scRNA-seq

value: primary leukemia sample

value: untreated


title: Atg5_cre_1

value: Lung

value: neutrophils


title: SJALL040053_D1 scRNA-seq


title: Mettl14KO_NPC,replicate4,m6A-seq

description:
Library name: Sample8
m6A-seq


title: adr-2(-) neural cells biol rep 1

description: Library name: Sample 1_GSF3747


title: WGP day 1, LPS-treated day 7, mouse 4

city: Dublin

first: Roger

last: Preston

state: Dublin

address: 123 St Stephen's Green

country: Ireland

institute: Royal College of Surgeons in Ireland (RCSI)

data_processing:
Raw data from RNA sequencing was then bioinformatically processed in-house by Novogene. Briefly, this included quality control of reads where read removed if they included adaptor contamination, >10% of bases were resolved as uncertain (N), and where >50% of bases had a base quality < 5.
All samples had >97% of bases with a Q Phred values greater than 20, and over 93% of bases with a Q Phred value greater than 30.
With these filtered samples and reads, reads were aligned to the mouse GRCm38 reference using HISAT269 to generate gene counts.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited file containing the raw gene counts for each sample.

source_name: Bone marrow

extract_protocol:
Cells were washed once with PBS, and cells were lysed with lysis buffer (Ambion PureLinkTM RNA isolation kit) containing 1% 2-mercaptoethanol. Total RNA was isolated according to the manufacturer’s instructions. RNA samples were purified using RNeasy PowerClean Pro Cleanup Kit (Qiagen).
Sample QC, RNA library preparation and QC were performed in-house by Novogene, Cambridge.

treatment_protocol: We treated murine bone marrow derived macrophages (BMDMs) with whole glucan particle (WGP). After this cells were left for a rest period of 7 days before being rechallenged with lipopolysacharide (LPS). We then isolated RNA from untreated BMDMs, LPS-treated BMDMs and WGP+LPS BMDMs and performed RNA sequencing to compared gene expression between these treatment groups

value: Bone marrow

value: Primary Cells

value: bone marrow derived macrophages

value: Wild type

value: Whole glucan-particle and LPS treated


title: WGP day 1, LPS-treated day 7, mouse 3


title: IP_WT_3XFlag_rep2

city: Wuhan

first: Xiaoli

last: Zeng

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description: Library name: Sample 8

data_processing:
ChIP-seq reads were trimmed for low-quality reads using Trimmomatic v0.38 by standard parameters.
Clean reads were mapped to the Nostoc sp. PCC 7120 = FACHB-418 by Bwa v0.7.15 by standard parameters.
Peaks were called using MACS2 software v2.1.1 by default parameters.
Assembly: Nostoc sp. PCC 7120-BA000019.2
Supplementary files format and content: bigWig

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: cyanobacterium

growth_protocol: The wild type and devH-flag strains were incubated with constant illumination (light density of 30 μmol·m-2·s-1) in the BG11 medium. Cultures in flasks were shaken at 180 rpm.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200–500 bp).
ChIP-seq libraries were prepared using the I NEXTFLEX® ChIP-Seq Library Prep Kit for Illumina® Sequencing from Bio Scientific.

value: cyanobacterium

value: wild type

value: normal laboratory culture conditions

tag: time

value: logarithmic phase

tag: chip antibody

value: anti-FLAG (Sigma)


title: SJALL040099_D1 scRNA-seq


title: WGP day 1, LPS-treated day 7, mouse 2


title: WGP day 1, LPS-treated day 7, mouse 1


title: Mettl14KO_NPC,replicate3,m6A-seq

description:
Library name: Sample7
m6A-seq

value: hypothalamic neural progenitor cells

value: Mettl14 Knockout


title: Mettl14KO_NPC,replicate2,m6A-seq

description:
Library name: Sample6
m6A-seq


title: In_WT_3XFlag_rep2

description: Library name: Sample 6


title: Neural ADR-1;adr-2(-) input biol rep 2

description: Library name: Sample 8_GSF3747

data_processing:
Reads were aligned to C. elegans reference genome using STAR (v.2.7.8a)
Differential gene expression analysis was performed using Feature counts and DeSeq2. For the RIP and input samples, a likelihood ratio test (LRT) was also performed as a part of the DeSeq2
Assembly: C. elegans WS275
Supplementary files format and content: .csv files include DeSeq2 analysis

growth_protocol: After hatching using bleaching, L1 animals were washed off plates and  pellets were made

extract_protocol:
For the RIP samples, after bleaching, crosslinked  pellets were made using liquid nitrogen and either lysates or immunoprecipitated samples were collected in Trizol (Invitogen) and purified using TURBO Dnase(Ambion) followed by RNA Clean and Concentrator kit (Zymo)
Poly-A selected mRNA library preparation was done using KAPA stranded library preparation kit

value: Worm lysate

value: neural adr-1;adr-1(-);adr-2(-)

value: Bleaching was performed to collect L1 animals and crosslinked pellets were made


title: IP_WT_3XFlag_rep1

description: Library name: Sample 7


title: adr-2(-) neural cells biol rep 3

description: Library name: Sample 3_GSF3747

value: L1 neural cells

value: Neural cells from worms

value: Bleaching was performed to collect L1 animals and neural cells were isolated and collected in trizol


title: Mettl14KO_NPC,replicate1,m6A-seq

description:
Library name: Sample5
m6A-seq


title: Untreated, mouse 4

value: Bone marrow

value: Primary Cells

value: Untreated


title: Neural ADR-1;adr-2(-) IP biol rep 2

description: Library name: Sample 6_GSF3747

source_name: L1 RIP

value: L1 RIP

value: ADR-1 RIP from worms


title: Neural ADR-1;adr-2(-) input biol rep 1

description: Library name: Sample 7_GSF3747


title: IP_devH_3XFlag_rep2

description: Library name: Sample 4

value: cyanobacterium

value: native devH replaced by an allele encoding a DevH variant tagged with FLAG at the C-terminus


title: Neural ADR-1;adr-2(-) IP biol rep 1

description: Library name: Sample 5_GSF3747


title: Control_NPC,replicate3,m6A-seq

description:
Library name: Sample3
m6A-seq

value: Control


title: Untreated, mouse 3

value: bone marrow derived macrophages

value: Wild type


title: Control_NPC,replicate2,m6A-seq

description:
Library name: Sample2
m6A-seq

value: hypothalamic neural progenitor cells


title: Untreated, mouse 2


title: Neural ADR-1 input biol rep 2

description: Library name: Sample 4_GSF3747

value: Worm lysate

value: neural adr-1;adr-1(-)


title: In_devH_3XFlag_rep2

description: Library name: Sample 2

value: normal laboratory culture conditions

value: logarithmic phase


title: Untreated, mouse 1


title: Control_NPC,replicate1,m6A-seq

description:
Library name: Sample1
m6A-seq


title: Neural ADR-1 input biol rep 1

description: Library name: Sample 3_GSF3747

value: Bleaching was performed to collect L1 animals and crosslinked pellets were made


title: In_devH_3XFlag_rep1

description: Library name: Sample 1


title: 96hCo_rep3

description:
Library name: Sample 18
Column name in FPKM_all_samples.txt: co-t96-3

data_processing:
Sequencing reads were trimmed for adapter sequences and low-quality reads using Trimmomatic v0.36 by standard parameters.
Trimmed sequence reads were mapped to Nostoc sp. PCC 7120 = FACHB-418 using HISAT2 2.2.1 by standard parameters.
Read count extraction and normalization were performed using StringTie v2.2.1 by standard parameters.
Assembly: Nostoc sp. PCC 7120-BA000019.2
Supplementary files format and content: Tab-delimited txt file includes FPKM values for each sample.

growth_protocol: The PcoaT-devH strain was cultured in the BG11 medium with cobalt to reach an exponential phase, followed by washing and inoculating from OD750 0.1 into BG11 in the presence or absence of cobalt.

extract_protocol:
Total RNA was harvested using Trizol Reagent (Invitrogen Life Technologies). rRNA was removed using Ribo-clean rRNA Depletion Kit Mega (Bacteria) (Vazyme).
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme) following the manufacturer's protocols.

treatment_protocol: Cells were harvested by rapid filtration and treated by RNAlater (RNA stabilization reagent) for 30 minutes at room temperature.

value: native promoter of devH replaced by the Co2+/Zn2+-inducible promoter (PcoaT)

value: cultured in BG11 medium with cobalt


title: Untreated day 1, LPS-treated day 7, mouse 3

value: Bone marrow

value: Primary Cells

value: LPS treated


title: Mettl14KO_NPC,replicate4,RNA-seq

description:
Library name: Sample8
bulk RNA-seq

data_processing:
Bulk sequencing data were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina) with adapter trimming using Trimmomatic v0.32 software (Bolger et al., 2014). Alignment was performed using STAR v2.5.2a (Dobin et al., 2013). GENCODE mouse reference genome GRCm38.p6 was used for alignment.
Assembly: mm10
Supplementary files format and content: raw counts, each file is a raw counts table for cells obtained from one sample

extract_protocol:
Total RNA fraction was isolated from cultured hypothalamic NPCs samples using RNA Clean & Concentration Kit. Enrichment of polyadenylated RNA from total RNA was performed using Oligo(dT) dynabeads according to the manufacturer’s protocol. The polyadenylated RNA was chemically fragmented into ∼80-nt-long fragments using zinc fragmentation reagent. To purify the RNA, 20 μl MyOne Silane Dynabeads were washed in 100 μl RLT, resuspended in 30 μl RLT, and added to the eluted RNA. 60 μl 100% ethanol was added to the mixture, the mixture attached to the magnet and the supernantant discarded. Following two washes in 100 μl of 70% ethanol, the RNA was eluted from the beads in 16.5 µl water.
50 ng of polyadenylated RNA fragments from Mettl14 knockout or control NPCs were used for cDNA library preparation with the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770S) following the manufacturer's protocol.Then the IP samples were used for cDNA library preparation with the NEBNext Ultra II RNA Library Prep Kit. Sequencing library fragment sizes were quantified by bioanalyzer with an average size of ∼400 bp, and concentrations were quantified by qPCR (KAPA). Samples were pooled, loaded at 2.7 pM, and sequenced on a Next-Seq 500 (Illumina).

value: Mettl14 Knockout


title: Mettl14KO_NPC,replicate3,RNA-seq

description:
Library name: Sample7
bulk RNA-seq


title: In_WT_3XFlag_rep1

description: Library name: Sample 5

value: cyanobacterium

value: wild type


title: Untreated day 1, LPS-treated day 7, mouse 2


title: 96hCo_rep2

description:
Library name: Sample 17
Column name in FPKM_all_samples.txt: co-t96-2


title: 96hCo_rep1

description:
Library name: Sample 16
Column name in FPKM_all_samples.txt: co-t96-1


title: Control_NPC,replicate4,m6A-seq

description:
Library name: Sample4
m6A-seq

value: Control


title: PAWTiron4

city: Sydney

first: M. Mozammel

last: Hoque

state: NSW

address: 15 Broadway, Ultimo

department: Australian Institute for Microbiology & Infection (AIMI)

country: Australia

institute: University of Technology Sydney

data_processing:
The RNA sequencing reads were filtered to remove adapter contamination and low-quality bases (≤ Q30) using TrimGalore and were checked using FastQC before analysis.
Clean reads were aligned to the reference genome using Subread aligner.
The mapped reads per gene count were quantified using featureCount.
The count matrices were uploaded to R version 4.2.0 and differential expression analysis was performed using edgeR.
Assembly: Escherichia coli ATCC 25922 (RefSeq accession number NZ_CP009072)
Supplementary files format and content: Count matrix

organism: Escherichia coli

source_name: biofilms

extract_protocol:
Lysozyme and proteinase K were utilised to enzymatically lyse and digest the E. coli biofilm cells, and RNA extracted as per RNeasy® Mini Kit manufacturer’s protocol (Qiagen).
The library preparation and ribosome depletion were carried out using the Illumina Stranded Total RNA prep Ligation with Ribo-Zero Plus kit according to the manufacturer’s protocol (Illumina, San Diego, CA, USA).

value: biofilms

value: Bubble-Tiron


title: IP_devH_3XFlag_rep1

description: Library name: Sample 3

value: native devH replaced by an allele encoding a DevH variant tagged with FLAG at the C-terminus

value: anti-FLAG (Sigma)


title: Mettl14KO_NPC,replicate2,RNA-seq

description:
Library name: Sample6
bulk RNA-seq

value: hypothalamic neural progenitor cells


title: Untreated day 1, LPS-treated day 7, mouse 1

value: bone marrow derived macrophages

value: Wild type


title: Mettl14KO_NPC,replicate1,RNA-seq

description:
Library name: Sample5
bulk RNA-seq


title: PAWTiron2


title: 72hCo_rep2

description:
Library name: Sample 14
Column name in FPKM_all_samples.txt: co-t72-2


title: M9, IRI

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

data_processing:
Demultiplexing, quality control, and preprocessing of the scRNA data was conducted with the BD Rhapsody Sequence Analysis Pipeline v.1.11 from SevenBridges.
Sequences were aligned against a targeted genome panel based on the murine reference mm10 with the BD Rhapsody. Sequence Analysis Pipeline v1.11
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney + peripheral blood

extract_protocol:
For intravascular leukocyte staining, a PE-labeled rat anti-mouse CD45.2 antibody (2µg) was injected intravenously via the vena cava of anesthezised mice. Subsequently, puncture site was covered with surgical hemostat to control venous hemorrhage. After 5 minutes of antibody incubation blood was collected by cardiac puncture and organs were harvested without perfusion. Heparinzed blood was incubated with Fc Block (CD16/32) for 10 min on ice followed by antibody staining for 30 min. Erythrocytes were lysed for 10 min at RT using 1x RBC Lysis/Fixation solution (Biolegend). Samples were washed with PBS at 400 xg for 5 min and cell pellets were resuspended in PBS with 1% FCS. Organs were minced into small pieces and kidney, liver and lung were digested in 1 mL HBSS (Ca/Mg) including DNAse I (10mg/mL) and Collagenase I (100 U/µL) at 37°C and 350 rpm for 30 min (kidney) or 45 min (liver and lung). Addition of 2ml PBS to all organs was followed by filtering suspensions trough a 70 µm cell strainer. Samples were then centrifuged at 400 xg for 5 min and cell pellets were resuspended in PBS with 1% FCS. Cells were incubated with antibody mixtures (1:100) for 30 min on ice. Red blood cell lysis was performed for spleen according to blood while other organs were fixed with 4% PFA for 10 min. Cells were washed with 2 ml PBS (400 xg, 5 min) and resuspended in PBS with 1% FCS.
Approximately 10,000-25,000 vital cells of each sample were processed for scRNA-seq using using BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (BD Biosciences, Cat. No. 633774) according to the manufacturer's instructions. Quality, purity, average size and concentration of copy DNAs and libraries were determined by measurements on a Qubit FLuorometer (Thermo Fisher Scientific) and a Tapestation 2200 (Agilent Technologies). Indexed libraries were sequenced using a NovaSeq 6000 sequencing platform with PE150. flow cell and reagents (Illumina).

treatment_protocol: Mouse model bilateral renal ischemia/reperfusion injury (IRI) were studied at day 12 (AKI-reg) post injury. Surgical procedure was performed as follows:  Buprenorphine (0.1mg/kg) was administerd subcutaneously to 8-20 week-old males 20 min before surgery. Mice were anesthesized with 1,5-2% isoflurane/oxygen mixture, placed on a thermoregulated pad to maintain body temperature and a midline abdominal incision was made. For IRI induction, renal pedicles were carefully dissected and clamped with an atraumatic vascular clamp for 30 min.

value: kidney + peripheral blood

value: wt

value: IRI

value: male

tag: age


title: Untreated day 1, LPS-treated day 7, mouse 4

value: Bone marrow

value: Primary Cells


title: Neural ADR-1 IP biol rep 2

description: Library name: Sample 2_GSF3747

value: L1 RIP

value: ADR-1 RIP from worms

value: neural adr-1;adr-1(-)

value: Bleaching was performed to collect L1 animals and crosslinked pellets were made


title: Control_NPC,replicate4,RNA-seq

description:
Library name: Sample4
bulk RNA-seq

value: Control


title: 72hCo_rep1

description:
Library name: Sample 13
Column name in FPKM_all_samples.txt: co-t72-1

value: cyanobacterium

value: native promoter of devH replaced by the Co2+/Zn2+-inducible promoter (PcoaT)

value: cultured in BG11 medium with cobalt


title: M8, IRI


title: PAW4

value: biofilms

value: treatment solution PAW


title: Control_NPC,replicate3,RNA-seq

description:
Library name: Sample3
bulk RNA-seq

value: hypothalamic neural progenitor cells


title: 48hCo_rep3

description:
Library name: Sample 12
Column name in FPKM_all_samples.txt: co-t48-3


title: Control_NPC,replicate2,RNA-seq

description:
Library name: Sample2
bulk RNA-seq


title: Neural ADR-1 IP biol rep 1

description: Library name: Sample 1_GSF3747


title: M5, untreated

value: kidney + peripheral blood

value: untreated


title: PAW3


title: 48hCo_rep2

description:
Library name: Sample 11
Column name in FPKM_all_samples.txt: co-t48-2


title: M4, IRI

value: wt

value: IRI


title: Control_NPC,replicate1,RNA-seq

description:
Library name: Sample1
bulk RNA-seq


title: 72hCo_rep3

description:
Library name: Sample 15
Column name in FPKM_all_samples.txt: co-t72-3


title: PAWTiron3

value: Bubble-Tiron


title: PAW2


title: 48hCo_rep1

description:
Library name: Sample 10
Column name in FPKM_all_samples.txt: co-t48-1


title: INPUT_ARCOD12

description:
Library name: Sample3
m6A-seq

data_processing:
*library strategy: m6A-seq
Raw sequencing data from m6A-seq were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina), and adaptors were trimmed using Trimmomatic v0.32 software with MINLEN(Bolger et al., 2014). Alignments were made using STAR v2.5.2a to GENCODE mouse reference genome GRCm38.p6 or the GENCODE human reference genome GRCh38.p13. All m6A modification sites were examined using the BAM file generated from STAR, applying exomePeak2 with criteria of fold change > 2 compared to input and FDR < 0.01).
Assembly: GRCh38.p13
Supplementary files format and content: m6A peak files from exomepeak2

source_name: iPSCs induced day 12 ARCOs

growth_protocol: Human iPSC colonies were detached with ReLeSR reagent for 5 mins, transferred to ultra-low Attachment U-bottom 96-well plates (20K cells/well) and cultured in mTeSR feeder-free maintenance media supplemented with 10 mM Y-27632 for 24 hours for Embryoid Body aggregation. On Day 2, EBs were transferred to an ultra-low attachment 6-well plate and maintained on a CO₂-resistant orbital shaker until day 12.

extract_protocol:
Total RNA fraction was isolated from day12 ARCO samples using RNA Clean & Concentration Kit. Enrichment of polyadenylated RNA from total RNA was performed using Oligo(dT) dynabeads according to the manufacturer’s protocol. The polyadenylated RNA was chemically fragmented into ∼80-nt-long fragments using zinc fragmentation reagent. To purify the RNA, 20 μl MyOne Silane Dynabeads were washed in 100 μl RLT, resuspended in 30 μl RLT, and added to the eluted RNA. 60 μl 100% ethanol was added to the mixture, the mixture attached to the magnet and the supernantant discarded. Following two washes in 100 μl of 70% ethanol, the RNA was eluted from the beads in 16.5 µl water. Enrichment of m6A modified RNA was obtained using polyadenylated RNA fragments from 30 µg total RNA with the EpiMark N6-Methyladenosine Enrichment Kit (NEB) following the manufacturer's protocol.
IP samples were used for cDNA library preparation with the NEBNext Ultra II RNA Library Prep Kit. Sequencing library fragment sizes were quantified by bioanalyzer with an average size of ∼400 bp, and concentrations were quantified by qPCR (KAPA)

treatment_protocol: Organoids were not treated with specific reagents prior to experiments.

value: iPSCs induced day 12 ARCOs

value: WT

value: input


title: M3, untreated

value: male


title: PAW1


title: BubbleTiron4

value: treatment solution Bubble-Tiron.


title: 96h_rep3

description:
Library name: Sample 9
Column name in FPKM_all_samples.txt: 11-c-z-t96-3


title: M2, untreated


title: ARCOD12, replicate2, m6A-seq

description:
Library name: Sample2
m6A-seq


title: PAWTiron1


title: 96h_rep2

description:
Library name: Sample 8
Column name in FPKM_all_samples.txt: 11-c-z-t96-2

value: cultured in BG11 medium without cobalt


title: ARCOD12, replicate1, m6A-seq

description:
Library name: Sample1
m6A-seq


title: M6, IRI


title: 96h_rep1

description:
Library name: Sample 7
Column name in FPKM_all_samples.txt: 11-c-z-t96-1

value: cyanobacterium


title: BubbleTiron3


title: M1, untreated


title: BubbleTiron2


title: BubbleTiron1


title: visual cortex, het male

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

data_processing:
Trimmomatic, version 0.39, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50
hisat2
optical duplicates removal, gatk-4.2.3.0, --OPTICAL_DUPLICATE_PIXEL_DISTANCE=12000
htseq-count, version 0.6.0, parameters: --stranded=reverse
Genome_build: GRCm38
Supplementary_files_format_and_content: counts generated by htseq-count

source_name: visual cortex

extract_protocol:
total RNA was extracted using phenol/chloroform
cDNA libraries were prepared using TruSeq™ Stranded Total RNA Library Prep (Illumina, USA) according to manufacturer’s procedure.

treatment_protocol: Visual cortex was dissected from the brains of mice at the age of P28

value: visual cortex

value: UTRmut/WT

value: P28 (postnatal day 28)


title: 72h_rep3

description:
Library name: Sample 6
Column name in FPKM_all_samples.txt: 11-c-z-t72-3

value: native promoter of devH replaced by the Co2+/Zn2+-inducible promoter (PcoaT)


title: 72h_rep2

description:
Library name: Sample 5
Column name in FPKM_all_samples.txt: 11-c-z-t72-2


title: visual cortex, WT male

value: WT/WT


title: OMM12, Spleen, Cl-13, 8 dpi

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

data_processing:
Read alignment and gene counting were performed with 10x Genomics Cell-Ranger v7.1. 0 (Zheng et al., 2017), using default parameters and pre-built mouse reference v2020-A (10x Genomics) based on mm10 GRCm38.p6 (release 98) and annotation from GENCODE Release M23. Downstream analysis was performed in R v4.3.0 with the R package Seurat v4.3.0 (Hao et al., 2021). Cells with >1,000 genes, <10% mitochondrial genes, and UMI counts within the values of the 2nd and 98th quantiles were retained, along with genes detected in ≥3 cells. Filtered read counts from each sample were normalized independently with sctransform v0.3.5 (Hafemeister and Satija, 2019) using the glmGamPoi method (Ahlmann-Eltze and Huber, 2021) and vst.flavor v2. Integration features were identified from top 1000 highly variable genes excluding mitochondrial, ribosomal and TCR genes before calculation. Anchors between cells from different sampleswere identified on the integration features using reciprocal PCA and selected using the first 20 dimensions and two neighbors. Data integration was performed considering 50 neighbors to weight the anchors. PCA was calculated for the integrated data on the top 1000 highly variable genes. Both KNN graph and UMAP (spread 1, min.distance 0.3) were computed on the 30 nearest neighbors and first 20 PCA dimensions. Louvain clusters were identified using the Shared nearest neighbor (SNN) modularity optimization-based algorithm at resolution 0.5. Differential expression was performed using the Wilcoxon Rank Sum test and Bonferroni correction
Assembly: mm10
Supplementary files format and content: Cell Ranger compressed files contain the filtered UMI counts matrix (Market Exchange Format for sparse matrices) and TSV files with genes and barcode sequences (corresponding to row and column indices respectively) as output by Cell Ranger.

source_name: Spleen

growth_protocol: Gnotobiotic mice were held in isolators

extract_protocol: Gene expression libraries for single cell RNA libraries were prepared from sorted virus-specific SMARTA cells by using the 10x Genomics pipeline and the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 according to the manufacture’s user guide

treatment_protocol: -5 d mice were injected with 5000 SMARTA cells and then 0 d mice were infected with LCMV Clone-13

tag: group

value: Spleen

tag: infection

value: 8 dpi


title: Bubble4

value: biofilms

value: treatment solution Bubble


title: 72h_rep1

description:
Library name: Sample 4
Column name in FPKM_all_samples.txt: 11-c-z-t72-1


title: 48h_rep3

description:
Library name: Sample 3
Column name in FPKM_all_samples.txt: 11-c-z-t48-3


title: GF, Spleen, Cl-13, 8 dpi

value: GF


title: visual cortex, Mmp9 UTRmut female

value: UTRmut/UTRmut

value: female


title: visual cortex, het female


title: Bubble2


title: GF, Small Intestine, Cl-13, 8 dpi

source_name: Small Intestine

value: Small Intestine


title: Bubble1


title: 48h_rep2

description:
Library name: Sample 2
Column name in FPKM_all_samples.txt: 11-c-z-t48-2


title: OMM12, Small Intestine, Cl-13, 8 dpi


title: visual cortex, Mmp9 UTRmut male

value: male


title: SPF, Spleen, Cl-13, 8 dpi

value: SPF


title: Replicate 2, High CAGA-GFP expression

status: Public on Mar 06 2025

city: Solna

first: Bernhard

last: Schmierer

state: (optional)

address: Biomedicum 9B, Solnavagen 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: NextSeq 1000/2000 Control Software 1.4.1.39716/RTA 3.9.25) with a 53nt(Read1)-10nt(Index1)-6nt(Index2) setup using 'P2' flowcell

data_processing:
Readcounts were mapped to the library sequences using MAGeCK/0.5.9.4
Assembly: GRCh38
Supplementary files format and content: tab-delimited .txt file with mapped readcounts
Library strategy: CRISPR screen, activation

source_name: Breast

growth_protocol: DMEM/10%FCS/100U/ml Pen/Strep

extract_protocol:
QIAamp DNA Blood Mini (Qiagen) according to manufacturer's instructions
PCR one amplicon with adaptor-containing primers

treatment_protocol: 48h with 5ng/ml TGF-beta1

value: Breast

value: CAGA-GFP

value: 5ng/ml TGFbeta


title: Replicate 2, Unsorted


title: Replicate 2, Low CAGA-GFP expression


title: 48h_rep1

description:
Library name: Sample 1
Column name in FPKM_all_samples.txt: 11-c-z-t48-1

value: cyanobacterium

value: cultured in BG11 medium without cobalt


title: Replicate 2, Early time point

value: Untreated


title: SPF, Small Intestine, Cl-13, 8 dpi


title: Replicate 1, High CAGA-GFP expression


title: Replicate 1, Early time point


title: Replicate 1, Low CAGA-GFP expression


title: MDA-MB-231,TGFb,eSNAI1,rep3

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
FastQ files were demultiplexed and processed using pipe4C (https://github.com/deLaatLab/pipe4C). Reads were mapped against hg38.  Read counts were normalized to one-million mapped intra chromosomal reads (normalized reads) excluding the two highest covered fragments and 21 fragment end rolling mean scores were calculated for every fragment end.
Assembly: hg38
Supplementary files format and content: Wig files
Library strategy: 4C-seq

growth_protocol: MDA-MB-231 cells were purchased from American Type Culture Collection (ATCC) and cultured in Dulbecco’s modified Eagle medium (DMEM; Thermo Fisher Scientific; 41965062) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific; 16000044) and 100 U/mL penicillin/streptomycin (Thermo Fisher Scientific; 15140163).

extract_protocol:
4C template preparation was performed as previously described in PMID: 31351925. In brief, five million cells per sample were cross-linked in 2% formaldehyde. Chromatin was digested in situ with DpnII (NEB, cat. no. R0543M) followed by dilution and ligation. Subsequently, crosslinks were removed by Proteinase K treatment, followed by template trimming using Csp6I (CviQI, Thermo Scientific, cat. no. ER0211) and re-ligation.
Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy using ELT PCR System (Roche, cat. no. 11681842001).

treatment_protocol: MDA-MB-231 cells were serum starved for 16 hours and stimulated without or with TGF-β (5 ng/mL) for 24 h.

value: TGFb

tag: vp

tag: replicate


title: Replicate 1, Unsorted


title: MDA-MB-231,TGFb,eSNAI1,rep2


title: Bubble3


title: MDA-MB-231,TGFb,eSNAI1,rep1


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_8

city: Ithaca

first: Iwijn

last: De Vlaminck

address: 237 Tower Road, Weill Hall 301

department: Biomedical Engineering

institute: Cornell University

data_processing:
Sequencing data was processed using a custom bioinformatics pipeline. Since pools sequenced on the Illumina NextSeq 2000 were optimized to produce paired-end, 61 bp reads, sequencing data from the Illumina NextSeq 500 and Novaseq 6000 were trimmed using Seqtk (v1.2).
Samples were then quality filtered and trimmed using BBDuk (v38.90), aligned to the Gencode GRCh38 human reference genome (v38, primary assembly) using STAR29 (v2.7.0f, default parameters).
Prior to feature quantification using featureCounts30 (v2.0.0), samples were deduplicated using Picard MarkDuplicates (v2.19.2). Mitochondrial, ribosomal, X, and Y chromosome genes were bioinformatically removed prior to analysis.
Samples were filtered on the basis of DNA contamination, rRNA contamination, total counts, and RNA degradation. DNA contamination was estimated by calculating the ratio of reads mapping to introns and exons. rRNA contamination was measured using SAMtools (v1.14). Total counts were calculated using featureCounts30 (v2.0.0). Degradation was estimated by calculating the 5’-3’ bias using Qualimap31 (v2.2.1).
Samples were removed from analysis if either the intron to exon ratio was greater than 3, if a sample had less than 75000 total feature counts, or if the rRNA contamination, total counts, or 5’-3’ bias was greater than 3 standard deviations from the mean.
Assembly: Gencode GRCh38 human reference genome (v38, primary assembly)
Supplementary files format and content: comma seprated values .csv file contain gene counts for each sample in this study

source_name: plasma from HSCT cohort

extract_protocol:
Before cfRNA extraction, plasma samples were thawed at room temperature and centrifuged at 1300 x g for 10 minutes at 4°C. cfRNA was extracted from the plasma supernatant (250-1500 μl) using the Norgen Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen, 51000). Extracted RNA was DNase treated with 14 μl of 10 μl DNase Turbo Buffer (Invitrogen, AM2238), 3 μl DNase Turbo (Invitrogen, AM2238), and 1 μl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37°C, then concentrated into 10 μl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Urine samples were thawed at room temperature and centrifuged at 16,000 x g for 10 minutes at 4 °C. cfRNA was extracted from (450-2000 μl) supernatant using QIAamp Circulating Nucleic Acid Kit -Purification of Circulating microRNA in serum/plasma/urine protocol (Qiagen, product #55114).  Extracted RNA was DNase treated with 14 μl of 10 μl DNase Turbo Buffer (Invitrogen, AM2238), 3 μl DNase Turbo (Invitrogen, AM2238), and 1 μl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37°C, then concentrated into 10 μl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Sequencing libraries were prepared from 8 µl of concentrated RNA using the Takara SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara, 634485) and barcoded using the SMARTer® RNA Unique Dual Index Kit (Takara, 634451). Library concentration was quantified using the Qubit™ 3.0 Fluorometer (Invitrogen, Q33216) with the dsDNA HS Assay Kit (Invitrogen, Q32854). Libraries were quality-controlled using the Agilent Fragment Analyzer 5200 (Agilent, M5310AA) with the HS NGS Fragment Kit (Agilent, DNF-474-0500) and pooled to equal concentrations. Each pool was sequenced using both the Illumina NextSeq 500/550 platform (paired-end, 150 bp) and the Illumina NextSeq 2000 platform (paired-end, 100 bp).

value: Plasma, extracted cell-free RNA

value: Hematopoietic Stem Cell Transplantation

tag: diagnosis


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_16


title: MDA-MB-231,NT,eSNAI1,rep3

value: NT


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_73


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_175

value: PR


title: MDA-MB-231,NT,eSNAI1,rep2


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_186

value: E


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_187


title: visual cortex, WT female

value: visual cortex

value: WT/WT

value: P28 (postnatal day 28)


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_177


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_176


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_158


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_161


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_156


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_157


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_155


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_108


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_84


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_131


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_160


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_114


title: Dorsal horn neurons, SNI-Ctrl #2

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

description:
Library name: P32110_1004
10x Genomics

data_processing:
Raw sequencing data were de-multiplexed, converted into fastq format, and aligned to mouse reference mm10 using the STAR aligner to generate the gene-cell matrices.
Assembly: mm10
Supplementary files format and content: .tsv files containing raw expression counts and corresponding metadata in separate .tsv (meta) files

source_name: Spinal cord, dorsal horn

extract_protocol:
Mice with a Cre dependent red fluorescent protein variant tdTomato reporter (10-20 weeks old, both males and females) were sacrificed with over dosage of isoflurane. Lumbar spinal cord was dissected out immediately and kept in freshly oxygenated artificial cerebrospinal fluid solution (modified ACSF: 87 mM NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 26 mM NaHCO3, 75 mM Sucrose, 10 mM Glucose, 0.5 mM CaCl2, 4 mM MgSO4) on ice. Gray matter from lumbar spinal dorsal horn (or only lumbar 4-6 from ipsilateral side) was dissected out and transferred to a plastic petri dish (3 cm) with 2 mL pre-warmed digestion enzyme in ACSF solution (Papain, 25 unit/mL and DNase I, 55 unit/mL, Worthington Biochemical). For spinal dorsal horn neuronal atlas construction, each experiment included 2-3 mice (BAF53b-Cre*R26Tom). For labeled active ensembles (FosdsTVA*R26Tom) or neurons from Sni mice (BAF53b-Cre*R26Tom), 4 mice were included for each suspension experiment. The following single cell suspension was performed according to our previous protocol (6) with modifications. Briefly, spinal cord tissues were cut into pieces and triturated (10 x up and down) every 10 min (4 x) using glass Pasteur pipettes with decreasing diameter (pre-coated with 0.5% BSA). Cell suspension was filtered through a 30 µm cell strainer (CellTrics, Sysmex) and washed with additional 1.5 mL ACSF and 0.5 mL PBS. Cells were spin down with centrifugation (300 g x 5 min, 4 °C) and resuspended with 2 mL ACSF. Cell suspension was carefully loaded on top of the same volume of OptiPrep density gradient medium (5.4% iodixanol in ACSF, Sigma) and centrifuge with 300 g x 10 min at 4 °C. Gradient centrifugation step was replaced with centrifugation (300 g x 5 min, 4 °C) for some samples. Cell pellet was resuspended with 4 mL ACSF. SYTOX Blue (Invitrogen, ThermoFisher Scientific) was added to stain dead cells. Then tdTomato positive and SYTOX Blue negative cells were sorted with fluorescence activated cell sorting (FACS) cell sorters (BD FACSAria Fusion / BD FACSAria III) at 4 °C. Cells were concentrated when necessary by centrifugation (300 g x 5 min, 4 °C) and resuspended with proper volume (~1000 cells/ µl) of ACSF solution.
Sorted cells were loaded onto the 10X Chromium chip G to yield single cell droplet with v3 or v3.1 kit (10X genomics). Targeted cell recovery for neuronal atlas construction or Sni samples was settled to 5000 cells, whereas the samples from captured active ensembles were aiming for 1000 cells. Reverse transcription, cDNA amplification and library construction were performed according to the user guide provided by manufacture.

value: Spinal cord, dorsal horn

value: Dorsal horn neuron and nonneuron

value: Control


title: Dorsal horn neurons, SNI-Ctrl #1

description:
Library name: P32110_1003
10x Genomics


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_67


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_20


title: MDA-MB-231,NT,eSNAI1,rep1


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_21


title: Dorsal horn neurons, SNI #2

description:
Library name: P32110_1002
10x Genomics

value: SNI


title: Dorsal horn neurons, SNI #1

description:
Library name: P32110_1001
10x Genomics


title: Dorsal horn neurons, ipsilateral, heat #2

description:
Library name: P24201_1003
10x Genomics

value: Heat


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_45


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_148


title: Dorsal horn neurons, contralateral

description:
Library name: P24201_1001
10x Genomics


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_15


title: Dorsal horn neurons, ipsilateral, heat #1

description:
Library name: P24201_1002
10x Genomics


title: GFP-Hepa(D14)-3

city: Shanghai

first: shitong

last: wang

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample42

data_processing:
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Assembly: Mus_musculus-NCBI-mm10;Homo_sapiens-NCBI-hg19
Supplementary files format and content: tab-delimited text files include GeneID and FPKM value

source_name: liver

extract_protocol:
Primary and expanded mouse hepatocytes were removed, flash frozen on dry ice, total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.
RNA library for RNA-seq was prepared as flows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library

value: liver

value: GFP induced hepatocytes (D14)

value: WT


title: GFP-Hepa(D14)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample41


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_143


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_149


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_95


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_109


title: BA-iHPCs(D14)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample39

value: Bhlha15 and Arntl2 induced hepatic progenitor cells (D14)


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_117

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_136

value: Hematopoietic Stem Cell Transplantation


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_123


title: HepaSTAT3-/- (IL22-HCM. D7)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample33

value: HepaSTAT3-/- (IL22-HCM. D7)


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_152


title: Hepa(D0)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample36

value: Primary hepatocytes (D0)


title: Hepa(D0)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample35


title: HepaSTAT3-/- (IL22-HCM. D7)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample32


title: Hepa(D0)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample34


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_91


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_68

value: PR


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_168

value: E


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_119


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_2


title: HepaSTAT3-/- (D0)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample27

value: HepaSTAT3-/- (D0)


title: HepaSTAT3-/- (IL22-HCM. D3)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample28

value: HepaSTAT3-/- (IL22-HCM. D3)


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_28


title: BA-iHPCs(D14)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample37


title: HepaSTAT3-/- (IL22-HCM. D3)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample30


title: HepaSTAT3-/- (IL22-HCM. D7)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample31


title: BA-iHPCs(D14)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample38


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_36


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_87


title: HepaSTAT3f/f (IL22-HCM, D7)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample24

value: HepaSTAT3f/f (IL22-HCM, D7)


title: HepaSTAT3-/- (IL22-HCM. D3)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample29


title: GFP-Hepa(D14)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample40


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_52


title: IL22-hiMHs(P5)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample51

value: IL22 induced human mature hepatocytes (P5)


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_5


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_65


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_106


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_7


title: HepaSTAT3f/f (IL22-HCM, D7)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample22


title: IL22-hiMHs(P5)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample50


title: HepaSTAT3f/f (IL22-HCM, D7)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample23


title: IL22-hiMHs(P5)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample49


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_120


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_4


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_90


title: HepaSTAT3f/f (IL22-HCM, D3)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample21

value: HepaSTAT3f/f (IL22-HCM, D3)


title: HepaSTAT3-/- (D0)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample25


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_89


title: IL22-hiHPCs(P5)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample48

value: IL22 induced human hepatic progenitor cells (P5)


title: HepaSTAT3-/- (D0)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample26


title: IL22-hiHPCs(P5)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample47


title: HepaSTAT3f/f (IL22-HCM, D3)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample20


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_125


title: IL22-hiHPCs(P5)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample46


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_3


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_88


title: HepaSTAT3f/f (IL22-HCM, D3)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample19


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_39


title: HepaSTAT3f/f (D0)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample18

value: HepaSTAT3f/f (D0)


title: hHepa(D0)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample45

value: liver

value: Primary human hepatocytes (D0)


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_35


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_18


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_80


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_97


title: hHepa(D0)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample44


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_93


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_56


title: HepaSTAT3f/f (D0)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample17

value: HepaSTAT3f/f  (D0)


title: HepaSTAT3f/f (D0)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample16


title: IL22-td-iMHs-mouse-2(P30)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample15

value: IL22 induced tdTomato positive mature hepatocytes (P30)-mouse-2

value: WT


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_135

value: Plasma, extracted cell-free RNA

value: Hematopoietic Stem Cell Transplantation


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_41


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_46


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_147


title: IL22-td-iMHs-mouse-2(P30)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample14


title: P5， placental vascular， Preeclampsia

city: Wuxi

first: Zhang

last: Eryun

state: jiangsu

address: 48 Huaishu Lane

institute: Wuxi Maternity and Child Health Care Hospital

description: Library name: sample 10

data_processing:
Disembarkation data quality control
Reference genome alignment
Methylation region recognition
Differential methylation region identification
Differential methylation region identification
Assembly: HG19
Supplementary files format and content: The table contains the DNA modification sites identified by each sample

source_name: placental vascular

extract_protocol:
MeDIP-Seq
5mC Antibody Immunoprecipitation (MeDIP) MeDIP experimental quality control MeDIP-DNA quantification

value: placental vascular

value: Preeclampsia


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_145


title: IL22-td-iMHs-mouse-2(P30)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample13


title: P4， placental vascular， Preeclampsia

description: Library name: sample 9


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_144


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_146


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_32

value: PR


title: IL22-td-iMHs-mouse-1(P30)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample12

value: IL22 induced tdTomato positive mature hepatocytes (P30)-mouse-1


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_44

value: E


title: IL22-td-iMHs-mouse-1(P30)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample11


title: P3， placental vascular， Preeclampsia

description: Library name: sample 8


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_47


title: P1， placental vascular， Preeclampsia

description: Library name: sample 6


title: P2， placental vascular， Preeclampsia

description: Library name: sample 7


title: hHepa(D0)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample43


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_92


title: IL22-td-iMHs-mouse-1(P30)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample10


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_30


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_99


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_101


title: C5， placental vascular， normal pregnancy

description: Library name: sample 5

value: normal pregnancy


title: C4， placental vascular， normal pregnancy

description: Library name: sample 4


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_59


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_29


title: C3， placental vascular， normal pregnancy

description: Library name: sample 3


title: IL22-td-iHPCs-mouse-2(P30)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample4

value: IL22 induced tdTomato positive hepatic progenitor cells (P30)-mouse-1


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_102


title: C2， placental vascular， normal pregnancy

description: Library name: sample 2


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_82


title: IL22-td-iHPCs-mouse-1(P30)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample9

value: IL22 induced tdTomato positive hepatic progenitor cells (P30)-mouse-2


title: C1， placental vascular， normal pregnancy

description: Library name: sample 1


title: IL22-td-iHPCs-mouse-2(P30)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample5


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_111


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_128


title: PMA/Iono ieILC1-like NK cells, IL-13-, Donor 43

city: Palo Alto

first: John

middle: B

last: Sunwoo

state: CA

address: 801 Welch Rd

department: Otolaryngology – Head & Neck Surgery

institute: Stanford School of Medicine

description:
Library name: Donor 43 IL-13-
Takara SMART-Seq mRNA

data_processing:
FASTQ files were processed via nf-core/rnaseq. Sequences were aligned with the STAR method and quantified via RSEM. Differential gene expression analysis (DGEA) was completed with the DESeq2 package.
Assembly: hg38
Supplementary files format and content: count files for each sample included as CSV file

source_name: ieILC1-like NK cells

growth_protocol: Peripheral blood NK cells were isolated from human LRS chambers using negative selection and density gradient centrifugation. Red blood cells were lysed with ACK lysing buffer. NK cells were cultured in RPMI 1640 supplemented with 10% FBS, 1% Pen Strep, 1% non-essential amino acids, 1mM sodium pyruvate, 10mM HEPES, 55µM 2-mercaptoethanol, and 10 ng/mL of IL-15.  ieILC1-like NK cells were produced by co-culturing peripheral blood NK cells with irradiated PCI-13 humnan HNSCC cells. PCI-13 cells were irradiated at 100 Gy. Co-culture was done with NK:PCI-13 cells at a 2:1 ratio in AIM-V media with 5% Immune Cell SR and 10 ng/mL of IL-15. Media was replaced every 2 days, and fresh PCI-13 cells after 4 days. At day 8, ieILC1-like NK cells were collected for subsequent assays.

extract_protocol:
RNA was extracted from purified cells via the QIAGEN RNeasy Plus Mini kit and then stored at -80°C.
Library prep was done by the company MedGenome. Library construction was made with Illumina Stranded mRNA Prep or Takara SMART-Seq mRNA.

treatment_protocol: NK cells were stimulated for 6 hours with PMA/Ionomycin (50 ng/mL PMA and 1 µg/mL Ionomycin). IL-13-expressing cells were identified using a IL-13 capture assay in which secreted IL-13 was captured by a cell surface-bound antibody. Cells with and without IL-13 captured at the cell surface were then sorted out.

value: ieILC1-like NK cells

value: PMA/Ionomycin

tag: batch

value: Donor 43


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_126


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_127


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_70


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_58


title: IL22-td-iHPCs-mouse-1(P30)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample7

value: liver


title: PMA/Iono ieILC1-like NK cells, IL-13+, Donor 43

description:
Library name: Donor 43 IL-13+
Takara SMART-Seq mRNA


title: IL22-td-iHPCs-mouse-2(P30)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample6


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_57


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_42


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_71


title: PMA/Iono ieILC1-like NK cells, IL-13-, Donor 35

description:
Library name: Donor 35 IL-13-
Takara SMART-Seq mRNA

value: Donor 35


title: IL22-td-iHPCs(D14)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample2

value: IL22 induced tdTomato positive hepatic progenitor cells (D14)


title: IL22-td-iHPCs(D14)-3

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample3

value: WT


title: PMA/Iono ieILC1-like NK cells, IL-13+, Donor 35

description:
Library name: Donor 35 IL-13+
Takara SMART-Seq mRNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_171

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_185

value: Hematopoietic Stem Cell Transplantation


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_184


title: PMA/Iono ieILC1-like NK cells, IL-13-, Donor 32

description:
Library name: Donor 32 IL-13-
Illumina Stranded mRNA Prep

value: Donor 32


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_170


title: PMA/Iono ieILC1-like NK cells, IL-13+, Donor 32

description:
Library name: Donor 32 IL-13+
Illumina Stranded mRNA Prep


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_179


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_83


title: IL22-td-iHPCs-mouse-1(P30)-2

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample8


title: IL22-td-iHPCs(D14)-1

address: 上海市浦东张江祖冲之路555号

institute: 中国科学院上海药物研究所

description: Library name: Sample1


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_182


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_183


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_151


title: Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna_150


title: HPR_174_input

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Pathology

institute: University of Michigan Medical School

description: Library name: Sample 152

data_processing:
Single-end or paired-end reads were aligned to hg19 using BWA-ALN (v 0.7.17).
Bam files were filtered (samtools view) to remove reads flagged as secondary alignments, not passing quality control, PCR or optical duplicates, and supplementary alignments (flags: 0x100, 0x200, 0x400, 0x800), and for paired-end read to retain only paired reads in a proper pair (flags: 0x1, 0x2)          .
Reads were filtered to retain only individual reads (single-end) or read-pairs (paired-end) mapping to <=2 sites genome-wide (X0 tag <=2 for single-end or both paired-end reads).
Display files were generated with deeptools bamCoverage (options: "--binSize 25 --normalizeUsing CPM --extendReads")
Assembly: hg19
Supplementary files format and content: bigwig (hg19 fragment coverage, normalized to fragments per million post-filtering)

source_name: Mass, base of tongue

extract_protocol:
For frozen lymphoma tumor samples, tumor cellularity from the frozen block was confirmed by H&E-frozen section by a board-certified hematopathologist (R.J.H. Ryan), and the block was trimmed as needed. Twenty-five–micron sections were then cut to a total of approximately 50 mg of tissue for each ChIP-Seq chromatin prep. Frozen sections were resuspended and dissociated in PBS + protease inhibitors + 10 mmol/L sodium butyrate. Formaldehyde was added to 1% and cells were cross-linked for 10 minutes at room temperature, quenched with 1/20th volume of 2.5M glycine, washed twice in cold PBS with protease inhibitors, and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40 + PI). Nuclei were pelleted at 3000g, and resuspended in cold SDS lysis buffer (0.3% SDS for H3K27ac and 1% SDS for TFs, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for 10 minutes. Nuclei were fragmented on a Q800R2 Sonifier (QSonica) as follows: three cycles of amplitude = 50, pulse times: 30s on / 30s off, total on time = 3:20 m, temperature = 80C. Samples were diluted 1:3 in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl +PI), and rotated at 4°C overnight with 2-5 ug of antibody. Antibody-chromatin complexes were captured with protein G–conjugated beads, washed, and eluted. After reversal of cross-linking, RNase and proteinase K treatment were performed and DNA was purified with Ampure XP beads for library preparation. Input sample was prepared by the same approach without immunoprecipitation.
ChIP DNA was end-repaired (End-It, Epicentre), A-tailed (Klenow fragment 3'-->5' exo-, New England Biolabs), and ligated (Quick T4 DNA ligase, NEB) to barcoded illumina adaptors (Single-Indexed Adapter Kit, KAPA, #KK8700). Each reaction was followed by clean-up with AMPure XP beads. Ligation products were amplified by PCR for 14-18 cycles with illumina indexing primers and PFU Ultra II HS PCR mix (Agilent). Library size selection to 300-600 bp was performed by two-step AMPure bead selection.

value: Mass, base of tongue

value: Diffuse large B-cell lymphoma


title: HPR_131_input

description: Library name: Sample 150

source_name: Lymph node, cervical

value: Lymph node, cervical


title: HPR_171_input

description: Library name: Sample 151

source_name: Mass, nasopharynx

value: Mass, nasopharynx


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-008

value: Urine, extracted cell-free RNA


title: Pool of cortices and hippocampi samples (2591, 2592, 2598 and 2789 mice)

city: Rehovot

first: Rafael

last: Valdés Mas

address: Herzl St 234

country: Israel

institute: Weizmann Institute

description: Library name: Batch_6

data_processing:
Ilumina output files were demultiplexed with bcl2fastq v.2.17. Resulting FASTQ files were analyzed using the zUMIs pipeline. Reads were aligned with STAR (v.2.5.3a) to the reference genome and unique molecular identifier (UMI) counts were used for downstream analysis.
the samples_description_barcode.tsv describes the barcodes for each sample in each batch
Assembly: Gencode_H34 or Gencode_M24/
Supplementary files format and content: tab delimited file including all gene counts across samples

source_name: Cortex, hippocampus

extract_protocol:
RNA was purified using standard chloroform extraction
Bulk mcSCRB-seq

value: Cortex, hippocampus

value: bulk

value: FAD/WT


title: Pool of cortices and hippocampi samples (2617, 2770 and 2783 mice)

description: Library name: Batch_9


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-003

source_name: urine from the HSCT cohort


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-021


title: Pool of cortices and hippocampi samples (2599, 2602, 2632 and 2755 mice)

description: Library name: Batch_7


title: Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna-097

value: PR


title: Pool of cortices and hippocampi samples (2588, 2589 and 2600 mice)

description: Library name: Batch_5


title: Pool of cortices and hippocampi samples (2754, 2788 and 2792 mice)

description: Library name: Batch_11