title: U2OS, siG6PC3, REP2

city: Copenhagen

first: Claus

middle: Storgaard

last: Sørensen

state: København N

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description: matrix column name: siG6PC3R2Aligned.sortedByCoord.out.bam

data_processing:
For data processing, FastqQC and FASTQ Screen were used to evaluate the reads quality. The adapter-trimmed reads were further quality trimmed with Fastp (v0.21.0) using default settings ('--disable_adapter_trimming --correction --trim_poly_x --cut_tail --trim_front1 12  --trim_front2 12 --trim_tail1 1 --trim_tail2 1').
Assembly: The trimmed reads were aligned to the hg38 genome assembly (canonical chromsomes only) using STAR (v2.7.3a) in two-pass mode and guided by a RefSeq (UCSC,2021/12/8) gene annotation (settings: --sjdbOverhang 133 --twopassMode Basic --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMunmapped Within --outFileNamePrefix siG6PC3R1 --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 25 --outFilterMismatchNmax 10 --peOverlapNbasesMin 20).
Supplementary files format and content: After mapping the reads were assigned to genes with featureCounts (v1.5.1, settings: -p -B -C -s 2 -J ) generating a count table.

source_name: U-2 OS

extract_protocol:
Cells were collected 48 hours after transfection following RNA extraction using AllPrep DNA/RNA Mini Kit (QIAGEN, 80204) on Qiacube MDX. Subsequently, RNA was subjected to DNase treatment with RNase-Free DNase Set (QIAGEN, 79254) and RNeasy Mini Kit (QIAGEN, 74106) on Qiacube MDX.
cDNA was converted and the libraries were pooled by Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit (Illumina, 20040529) according to the manufacturer’s protocol.
The sequencing was performed on Illumina NovaSeq 6000. The 150 bp paired-end RNA-seq data was base-called and adapter-trimmed with bcl2fastq by the sequencing facility to generate the raw fastq files.

value: U-2 OS

value: human osteosarcoma cell line

value: WT

value: G6PC3 small interfering RNA (siG6PC3) knockdown for 48h


title: 4_control_CEREBELLUM

status: Public on Apr 15 2025

type: SRA

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

country: USA

institute: Memorial SLoan-Kettering Cancer Center

library_source: transcriptomic

data_processing:
FastQ files of 2x100bp paired-end reads were quality checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 2012).
Samples were with high quality reads (Phred score >= 30) were aligned tothe Human reference genome (GRCh38/hg38) using STARaligner(version 2.7)55
Gene quantification was performed using feature counts from the Subread package in R56
Aligned reads were visualized using IGV (version 2.8.9).
Gene expression levels were normalized and log2 transformed using the Trimmed Mean of M-values (TMM) method
Differential expression analysis was performed using the edgeR package in R57. Significantly differentially expressed genes were selected with controlled False Positive Rate (B&H method) at 5% (FDR <= 0.05). Upregulated genes were selected at a minimum log2fold change of 2 and downregulated genes at a minimum log2fold change of -2
Heatmaps were drawn on the normalized expression matrix using the pheatmap package in R. Euclidean distance similarity metric and complete linkage algorithm were used for hierarchical clustering
Gene ontology (GO) and pathway (WikiPathways, KEGG, Reactome) analysis using g:profiler webtool was performed on the list of upregulated genes (log2>= 2 and FDR <=0.05) ordered by importance58. GO terms and pathways were selected based on an FDR <= 0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contains raw counts

molecule: polyA RNA

organism: Homo sapiens

source_name: brain

extract_protocol:
RNA was extracted from frozen tissue using the Qiagen all-prep DNA/RNA mini kit (80204) according to the manufacturer’s instructions
500 ng of total RNA was used for polyA selection and Truseq library preparation according to the instructions provided by Illumina (TruSeq RNA Sample Prep Kit v.2), with 8 cycles of PCR
TruSeq RNA Sample Prep Kit v.2

tag: tissue

value: brain

tag: cell line

value: Cerebellum

tag: cell type

value: Control


title: sgctrl_2_merge

city: Shanghai

first: Chen

last: Wang

address: Xianxia Rd 1111, Changning District

department: Department of Gastroenterology

country: China

institute: Shanghai Jiaotong University School of Medicine Affiliated Tongren Hospital

description: sgctrl_rep2 (FPKM)

data_processing:
Raw data were aligned using HISAT2 v2.2.1 against the hg38 version of the human genome.
For quantification of RNA-seq data, read counts and fragments per kilobase million (FPKM) values for each sample were calculated using StringTie v2.0.4.
Assembly: hg38
Supplementary files format and content: FPKM values for each sample

molecule: total RNA

growth_protocol: The human colorectal cancer cell line HCT15 was cultured in RPMI-1640 medium supplemented with 1% penicillin/streptomycin and 10% FBS at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA from control HCT15 and RBM15-knockout HCT15 cell lines was extracted using TRIzol.
RNA sequencing (RNA-seq) libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina and subjected to a paired-end 150 bp sequencing run on the Illumina NovaSeq 6000.

value: human colorectal cancer cells

tag: genotype


title: 3_control_CORTEX

value: Cortex


title: M2621-VE-BS-2mo

data_processing:
FastQ files of 2x100bp paired-end reads were quality checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 2012).
Samples were with high quality reads (Phred score >= 30) were aligned tothe Mouse reference genome mm10 using STARaligner(version 2.7)55
Gene quantification was performed using feature counts from the Subread package in R56
Aligned reads were visualized using IGV (version 2.8.9).
Gene expression levels were normalized and log2 transformed using the Trimmed Mean of M-values (TMM) method
Differential expression analysis was performed using the edgeR package in R57. Significantly differentially expressed genes were selected with controlled False Positive Rate (B&H method) at 5% (FDR <= 0.05). Upregulated genes were selected at a minimum log2fold change of 2 and downregulated genes at a minimum log2fold change of -2
Heatmaps were drawn on the normalized expression matrix using the pheatmap package in R. Euclidean distance similarity metric and complete linkage algorithm were used for hierarchical clustering
Gene ontology (GO) and pathway (WikiPathways, KEGG, Reactome) analysis using g:profiler webtool was performed on the list of upregulated genes (log2>= 2 and FDR <=0.05) ordered by importance58. GO terms and pathways were selected based on an FDR <= 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file contains raw counts

organism: Mus musculus

source_name: brain brainstem

growth_protocol: For targeting of BRAF(V600E) mutation to microglia progenitors, we genetically targeted EMPs by pulse-labelling  Cx3cr1CreER;Braf LSL-V600E E9.5 embryos ( with a single injection of 37.5 mg per kg (body weight) of 4-hydroxytamoxifen  into pregnant females.

extract_protocol:
RNA isolation was performed with Qiagen all-prep DNA/RNA mini kit (80204) according to the manufacturer’s instructio
total RNA underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S4 Reagent Kit (200 cycles) (Illumina).  An average of 29 million paired reads were generated per sample, the percent of mRNA bases per sample ranged from 47% to 85%, and ribosomal reads averaged 0.4%.
SMART-Seq v4 Ultra Low Input RNA Kit

value: brain brainstem

value: tissue

value: microglia

value: Braf VE; CX3 HET

tag: treatment

value: 2 months


title: U2OS, siG6PC3, REP3

description: matrix column name: siG6PC3R3Aligned.sortedByCoord.out.bam


title: U2OS, siUNC, REP2

description: matrix column name: siUNCR2Aligned.sortedByCoord.out.bam

value: Scramble siRNA without any targeting gene in human (siUNC) knockdown for 48h


title: 2_control_CORTEX


title: 4_control_CEREBELLUM2


title: NIH3T3_G4access_Starved_rep3

city: Montpellier

first: Amal

last: Makrini

address: 1919 route de mende

country: France

institute: IGMM

description:
Starved
NIH3T3_G4acces_starved_merge_bin10.wig

library_source: genomic

data_processing:
Mnase-seq , DNAse-seq and ChIP-seq samples were aligned to human genome (hg19, GRCh37) using Bowtie 2 aligner. Samples were then treated using PASHA pipeline to produce wig files (Fenouil et al. 2016). Uniquely aligned tags were elongated after estimating optimal elongation size in silico for single ended sequencing or between the pairs for paired end sequencing, enabling to use the original fragment length for further processing. Signals were scaled according to the mean signal. The number of tags covering each nucleotide of the genome was computed and averaged in bins of 10 or 50 nucleotides. For MNase-seq datasets, signals were smoothed on 5 bins.
RNA-seq samples were aligned to human genome (hg19, GRCh37)  and ERCC  reference using tophat2 aligner.
TT-seq samples were aligned to human genome (hg19, GRCh37)  and Drosophila melanogaster (DM6)  reference using tophat2 aligner.
Assembly: hg19
Supplementary files format and content: wig

molecule: genomic DNA

growth_protocol: Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/mL) and glutamin (2 mg/ml) at 37°C and 5% CO2.  NIH-3T3 cells were grown in DMEM supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/L) and glutamin (2.9 mg/L) at 37°C and 5% CO2.

extract_protocol:
Fifty million cells were used to perform each Pol II ChIP-seq experiments. Cells were crosslinked for 10 min at 20°C with the crosslinking solution (10 mM NaCl, 0.1 mM EDTA pH 8, 0.05 mM EGTA pH 8, 5 mM HEPES pH 7.8 and 1% formaldehyde). The reaction was stopped by adding glycine at a final concentration of 250 mM. After 5 min of formaldehyde quenching, cells were washed twice with cold PBS and resuspended in cold 2.5L LB1 (50 mM HEPES pH 7.5, 140 mM NaCl,1 mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) at 4°C for 20 min on a rotating wheel. Nuclei were pelleted down by spinning at 1350 rcf in a refrigerated centrifuge and washed in 2.5L LB2 (200 mM NaCl, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, 10 mM Tris pH 8) for 10 min at 4°C on a rotating wheel followed by centrifugation to collect nuclei. Nuclei were then resuspended in 1L LB3 (1 mM EDTA pH 8, 0.5 mM EGTA pH8, 10 mM Tris pH8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using Bioruptor Pico (Diagenode) in 15L tubes for 20 cycles of 30 s ON and 30 s OFF pulses in 4°C bath. All buffers (LB1, LB2 and LB3) were complemented with EDTA free Protease inhibitor cocktail (Roche), 0.2 mM PMSF and 1 µg/L Pepstatin just before use. After sonication, Triton X-100 was added to a final concentration of 1% followed by centrifugation at 20000 rcf and 4°C for 10 min to remove particulate matter. For sequencing of nucleosomal DNA in Raji cells, 35 million cells were resuspended in 350μl Solution I (150 mM sucrose, 80 mM KCl, 5 mM K2HPO4, 5 mM MgCl2, 0.5 mM CaCl2, 35 mM HEPES pH 7.4) and NP40 was added to a final concentration of 0.2%. Cell membranes were permeabilized for five min at 37°C. MNase was prepared at 50, 25, 12, 6 or 3 units in 0.5L of Solution II (150 mM sucrose, 50 mM Tris pH 8, 50 mM NaCl, 2 mM CaCl2) and incubated with 50 µL of cellular preparation, corresponding to 5. million cells, for exactly 10 min at 37°C. The reactions were stopped by adding of EDTA to a final concentration of 10 mM. The cells were lysed using 1.45L of SDS Lysis Buffer (1% SDS, 10 mM EDTA pH 8, 50 mM Tris pH 8), with 10 min incubation at 4°C. 200μl aliquots were taken for purification and the remaining extracts were stored at -80°C. An equal volume of TE (200ul) was added to the aliquots, followed by subsequent 2 hour treatments with each 0.2µg/L final concentrations of RNase A and Proteinase K at 37°C and 55°C, respectively. DNA was extracted by two subsequent phenol:chloroform:isoamylalcohol (25:24:1) extractions, further purified using QIAquick PCR purifications colums (Qiagen, Germany). Nucleosomal digestion was verified by running 500ng of DNA on a 1.5% agarose gel as well as on DNA high-sensitivity 2100 Bioanalyzer chips (Agilent, USA). Digestions showing 75% of mononucleomes (running at 150bp) were selected for library preparations. Chromatin RNA fraction was prepared from ∼20 million Raji cells. Cells were washed with ice-cold PBS twice. The cells were lysed with ice-cold 4 ml of HLB/NP40 buffer (10 mM Tris-Hcl, pH 7.5, 10 mM NaCl, 0.5% NP40, and 2.5 mM MgCl2) and incubated on ice for 5 min. After the incubation, 1 ml of ice-cold HLB/NP40/Sucrose buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP40, 2.5 mM MgCl2, and 10% Sucrose) was under-laid and then the nuclei were collected under 1,400 rcf centrifuge at 4°C for 5 min. Isolated nuclei were resuspended in 125 μl of NUN1 solution (20 mM Tri-HCl, pH 8.0, 75mM NaCl, 0.5 mM EDTA, 50% Glycerol) followed by 1.2 ml NUN2 buffer (20 mM HEPES-KOH pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% NP40). Fifteen minutes incubation was carried out on ice with mixing by max speed vortex for 5 s every ∼4 min and then chromatin pellets were precipitatd under 15,000 rcf centrifuge at 4°C for 10 min. Chromatin pellet was resuspended in 500 μl NUN2 buffer. Chromatin were precipitated under 15,000 rcf centrifuge at 4°C for 10 min, then Chromatin RNAs were extracted by 500 μl of Trizol reagent (Life technologies). The RNA extraction steps were repeated three times with rigorous treatment with TurboDNase in beetween. For DNase I sensitivity mapping, nuclei were prepared from 5 millions Raji cells per sample and incubated for 10 min at 37 °C with limiting concentrations of the DNA endonuclease DNase I (Sigma) supplemented with Ca2+ and Mg2+. A dose response experiment of 16 samples was performed with 2X dilution of the DNaseI between samples in cascade. Digestion was stopped by the addition of EDTA, and the samples were treated with proteinase K. The small fragments (<500 bp in length) were recovered on agrose gel from the sample in which a smear just started to appear using Quiagen gel purification kit and librairies were prepared using illumina Truseq kit. G4access was performed in K562 and NIH3T3 cells. Cells were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). For each experiment, 5 millions cells per titration point were re-suspended in 50 μL of prewarmed permeabilization buffer (150 mM of sucrose, 80 mM KCl, 5 mM KH2PO4, 5 mM MgCl2, 0.5 mM CaCl2 and 35 mM HEPES pH 7.4) supplemented with 0.2% (v/v) NP40 and incubated for 5 minutes at 37ºC prior digestion. MNase digestions, were then performed by adding a volume of 500 μL of prewarmed MNase reaction buffer (150 mM sucrose, 50 mM Tris-HCl pH 8, 50 mM NaCl and 2 mM CaCl2) supplemented with either 3, 6, 12, 25 or 50U of MNase (Merck, 10107921001). Digestions were incubated at 37ºC for 10 min and stopped on ice and by adding 11 μL of 500 mM EDTA to each reaction. Samples were then incubated 10 minutes on ice with 550 μL of SDS lysis buffer (1% (v/v) SDS, 10 mM EDTA and 50 mM Tris.HCl pH 8). Before DNA purification, 1 mL of water was added to dilute the SDS and the samples were incubated with 5 µL of RNAse A (ThermoFisher, EN0531) at 37 ºC for 2 hours and with 8 µL of proteinase K (Euromedex, 09-0911) at 56 ºC for 2 hours to complete the lysis. To then quality control the MNase digestions: 125 μL of each sample were cleaned-up using QIAquick PCR Purification Kit (QIAGEN, 28106) and assessed by agarose gel and Bioanalyzer. At this step, for efficient G4access, samples should present ~30% (+/-5%) of mono-nucleosomes. Importantly, this assessment should be performed on purified DNA that does not contain the subnucleosomal fraction, using a bioanalyzer equipment. The remaining of the samples was then purified by phenol-chloroform and ethanol precipitation for subsequent steps. We recommend that, when implementing this method, a wide range of MNase concentrations shall be tested in a first round of preparative experiments to narrow down the condition in which the critical fraction of 30% of mononucleosome shall be obtained. Our experiences showed this fraction is on average optimal for best G4 sequence recovery. The 0-100 bp size-selected fragments from MNase digestions that have ~30% of mono-nucleosomes were subjected to DNA library preparation. In parallel, genomic DNA libraries were sonicated by Bioruptor® Pico sonicator (Diagenode) to obtain DNA fragments of ~150 bp to be used later as reference data sets for bioinformatic analyses. Paired-end libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645S) using a starting material of 50 ng. DNA fragments were treated with end-repair, A-tailing and ligation of Illumina-compatible adapters. Clean-up of adaptor-ligated DNA was performed by using CleanNGS beads (CNGS-0050) with a bead:DNA ratio of 2:1. The purified products were amplified with 8 cycles of PCR. Finally, samples were cleaned up with a bead:DNA ratio of 0.8:1 to remove the free sequencing adapters.  TT-seq experiments were performed in biological duplicates using 47 millions Raji cells treated with 10 μM pyridostatin (PDS; Sigma SML0678) or H2O (Control) for 10 minutes. Newly synthetised RNAs were labelled with 500µM 4-Thiouridine (4SU; Sigma T4509) for 10min at 37°C at the time of the treatment. In parallel, 60 x106 drosophila S2R+ cells were labelled for 10min with 500µM 4SU. Cells were then harvested by centrifugation and Total RNA was isolated with QIAzol reagent (QIAGEN) according to the manufacturer’s instructions. Drosophila RNA was used as spike-in and added to Raji TotRNAs (1:40 ratio). TotRNAs were fragmented (two-times 105µg in 120µL) using a Covaris sonicator M220 (7°C, Power 75W, Duty factor 1%, burst 200) to generate RNA fragments of 200bp to 10kb. 4SU-labeled RNA from 210µg of Fragmented RNA was biotinylated, pulled-down using streptavidin beads and eluted with freshly prepared 100mM DTT. 4sU-labeled RNA (TT-seq) were treated with RNase-free DNase I, purified with miRNeasy MinElute spin column and eluted in 15µL Nuclease-free water. Prior to library preparation, samples were quantified with Nanodrop and quality was assessed by Bioanalyzer Nano RNA ChIP. Ribosomal RNA were depleted from samples using NEBNext rRNA Depletion Kit V2 (NEB ; E7400) and sequencing libraries were prepared with NEBNext Ultra II Directional Kit (NEB, E7760) according to manufacturer’s instructions.
ChIP-seq, RNA-seq
Mnase-seq, DNase-seq and ChIP-seq librairies were prepared using Illumina's ChIP Sample Prep Kit according to standard protocol. ChrRNA-seq librairies were prepared using Illuminas's "TruSeq® Stranded Total RNA Library Prep Gold (ref. 20020599)" kit according to standard protocol. TT-seq librairies were prepared using NEBnext Utra II Directional Kit.

treatment_protocol: For the α-amanitin experiments, cells were treated with 2.5 µg/mL at the indicated times. For the Pyridostatin experiments, cells were treated with 10 µM pyridistatin. For Triptolide treatment,  Raji cells were treated for 2h with 1 µM. For serum stimulation, cells were starved overnight in DMEM/0.3% FCS before stimulation with 15%FCS for 15minutes.

value: Fibroblast

tag: strain

value: Embryo

tag: experiment

tag: spike-in reference organisme

value: Drosophila melanogaster

tag: spike-in cell line

tag: chip antibody

value: Overnight starvation in DMEM+0.3% FCS


title: M2621-VE-Cort-2mo

source_name: brain cortex

value: brain cortex


title: M2624-VE-BS-2mo


title: Mm_thymus_B6_P28_Foxn1KO_rep1

city: Freiburg

first: Thomas

last: Boehm

address: Stuebeweg 51

department: Developmental Immunology

country: Germany

data_processing:
Transcriptomes were analyzed on the Galaxy platform.
Adapters were trimmed with TrimGalore! (version 0.4.3.1).
Reads were aligned to the reference genome with Hisat2  (version 2.1.0).
Counts were generated with featureCounts (version 1.6.1.0).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample

source_name: thymus

extract_protocol:
Preparations of single TECs were prepared from explanted thymi. Negative enrichment via MACS sorting with anti-CD45 beads (Miltenyi) was performed. Enriched TECs were purified by FACS and sorted directly into TRI reagent (Sigma-Aldrich). RNA was extracted following standard protocols.
Libraries were constructed with the NEBNext Ultra RNA Library Prep kit or the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.

value: thymus

value: Epcam+CD45- TECs

tag: age

tag: condition


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBG promoter, rep2, bin4

city: St. Louis

first: Barak

last: Cohen

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

description: Library name: DLP1_HBG_0kb_10kb_GATA1_library_rep2_bin4

data_processing:
We parsed the enhancer barcode (eBC), distance barcode (dBC) and random barcode (rBC) from each read in the fastq files and counted the abundance of each eBC-dBC-rBC combination to generate the barcode_summary.txt files.
We filtered out eBC-dBC-rBC combinations with <= 20 reads to remove under-sequenced integrations or potential sequencing errors, and then only kept eBC-dBC pairs with >= 10 unique rBCs to make sure every enhancer at every distance was measured from at least 10 independent integration events.
After filtering, we collapsed all rBCs associated with certain eBC-dBC pairs. We normalized the read counts by the total reads in each bin and then renormalized each barcode across bins to get barcode distribution probability. We used the distribution probability and the median mScarlet fluorescence of each bin to calculate the weighted average mScarlet level of each eBC-dBC pair. To compare enhancer activities across different distances, we normalized the calculated mScarlet level by the mScarlet level of the basal promoter with no enhancer or with scrambled controls.
Assembly: hg38
Supplementary files format and content: barcode_summary.txt files: A tab-delimited txt file containing raw read counts of every unique eBC-dBC-rBC combination. 1st column: name of the enhancer; 2nd column: E-P distance; 3rd column: rBC sequence; 4th column: read count

growth_protocol: K562 cells were grown in IMDM (Isocove's Modified Dulbecco's Medium) supplemented with 10% fetal bovine serum (FBS), 1% non-essential amino acids (NEAA) and 1% penicillin/streptomycin (pen/strep).

extract_protocol:
Genomic DNA was extracted from each sorted population using Qiagen DNA mini kit (Qiagen, #51304).
For each of the genomic DNA sample, we performed 8 separate 50ul reactions with lr_P3:  GCATGCGAATGGCCTCGTAG and lr_P5: CACAGCCAGACCAACATTGCC using the following condition: 98 °C for 30 s; 20 cycles of 98 °C for 15 s, 69 °C for 15 s and 72 °C for 45 s. After PCR, we pooled eight PCRs for each sample, cleaned up DNA using 1.2x SPRIselect beads(Beckman Coulter, B23317) and quantified DNA concentration using Qubit (Invitrogen, Q33231). We added sequencing adapters and indices with two additional rounds of PCRs: for PCR2, we took 4ng PCR1 product as template and performed 8 cycles of PCR with primers lr_P4: CTTTCCCTACACGACGCTCTTCCGATCTGCATGCGAATGGCCTCGTAG and lr_P6: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCACAGCCAGACCAACATTGCC. For PCR3, we took 2ul PCR2 product as template and amplified another 8 cycles using primers IDT_10_i5: AATGATACGGCGACCACCGAGATCTACAC(10bp index)ACACTCTTTCCCTACACGACGCTC and IDT_10_i7: CAAGCAGAAGACGGCATACGAGAT(10bp index)GTGACTGGAGTTCAGACGTG. After PCR3, we cleaned up DNA using 1.2x SPRIselect beads and quantified DNA concentration using Qubit. (Invitrogen, Q33231).

treatment_protocol: Pooled K562 long-range landing pad cells were transfected with Flpase recombinase along with the enhancer library. After 3 days, the transfected cells were treated with 2uM Ganciclovir for 7 days. The survived cells were allowed to grow for another 4 days and then FACS sorted on Day14 into four bins based on the mScarlet fluorescence levels. We collected 1.5 million cells from each sorted population.

value: Pooled 0kb and 10kb long-range landing pad cells with HBG promoter

value: integrated with GATA1/non-GATA1 enhancer library


title: U2OS, siUNC, REP3

description: matrix column name: siUNCR3Aligned.sortedByCoord.out.bam

value: U-2 OS

value: human osteosarcoma cell line

value: WT


title: Mm_thymus_B6_P28_Foxn1KO_rep2

institute: Max Planck Institute for Immunobiology and Epigenetics


title: 3_control_CEREBELLUM

value: brain

value: Cerebellum

value: Control


title: 2_control_HIPPOCAMPUS

value: Hippocampus


title: M2624-VE-Cort-2mo

value: tissue

value: microglia

value: Braf VE; CX3 HET

value: 2 months


title: U2OS, siUNC, REP1

description: matrix column name: siUNCR1Aligned.sortedByCoord.out.bam

value: Scramble siRNA without any targeting gene in human (siUNC) knockdown for 48h


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBG promoter, rep2, bin2

description: Library name: DLP1_HBG_0kb_10kb_GATA1_library_rep2_bin2


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBG promoter, rep2, bin3

description: Library name: DLP1_HBG_0kb_10kb_GATA1_library_rep2_bin3


title: 1_control_BRAINSTEM

value: Brainstem


title: 1_control_CEREBELLUM


title: M2629-Ctrl-BS-2mo

value: brain brainstem

value: Braf WT; CX3 HET


title: U2OS, siG6PC3, REP1

description: matrix column name: siG6PC3R1Aligned.sortedByCoord.out.bam

value: G6PC3 small interfering RNA (siG6PC3) knockdown for 48h


title: Raji_TT-seq_T10_PDS_rep2

description:
Treated with 10 µM Pyridostatin
Raji_TT-seq_T10_PDS_merge_normalized_pos_bin50_smoothed.wig
Raji_TT-seq_T10_PDS_merge_normalized_neg_bin50_smoothed.wig

source_name: Raji B cells

value: B lymphocyte

value: Burkitt's lymphoma

value: Raji

value: TT-seq

value: Drosophila melanogaster

value: Pyridostatin for 10 minutes

tag: concentration

value: 10 uM Pyridostatin

tag: duration

value: 10 minutes


title: Raji_TT-seq_T0_PDS_rep2

description:
untreated
Raji_TT-seq_T0_PDS_merge_normalized_pos_bin50_smoothed.wig
Raji_TT-seq_T0_PDS_merge_normalized_neg_bin50_smoothed.wig

value: untreated


title: M2629-Ctrl-Cort-2mo

value: brain cortex

value: tissue

value: microglia


title: M2617-VE-Cort-2mo

value: Braf VE; CX3 HET

value: 2 months


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBG promoter, rep1, bin4

description: Library name: DLP1_HBG_0kb_10kb_GATA1_library_rep1_bin4

value: Pooled 0kb and 10kb long-range landing pad cells with HBG promoter

value: integrated with GATA1/non-GATA1 enhancer library


title: Raji_TT-seq_T10_PDS_rep1


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBG promoter, rep2, bin1

description: Library name: DLP1_HBG_0kb_10kb_GATA1_library_rep2_bin1


title: Raji_TT-seq_T0_PDS_rep1


title: M2618-Ctrl-BS-2mo

value: brain brainstem

value: Braf WT; CX3 HET


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBG promoter, rep1, bin3

description: Library name: DLP1_HBG_0kb_10kb_GATA1_library_rep1_bin3


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBG promoter, rep1, bin2

description: Library name: DLP1_HBG_0kb_10kb_GATA1_library_rep1_bin2


title: Raji_Mnase-seq_Triptolide_2

description:
Treated with 10 µM Pyridostatin
Raji_Mnase-seq_Triptolide_merge_bin10.wig

value: B lymphocyte

value: Burkitt's lymphoma

value: MNase-Seq

value: Tryptolide for 2 hours

value: 1 uM Triptolide

value: 2 hours


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBG promoter, rep1, bin1

description: Library name: DLP1_HBG_0kb_10kb_GATA1_library_rep1_bin1


title: M2618-Ctrl-Cort-2mo


title: Raji_Mnase-seq_Triptolide_1

value: Raji


title: Fib_CD8+CLA+CD103neg_PAM126

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: Fibroblasts

extract_protocol:
High-quality total RNA was isolated from approximately 2 x 104 T cell supernatant-treated keratinocytes or fibroblasts using TRIzolTM Reagent (InvitrogenTM; 15596026). cDNA was prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara).
Library construction was performed using the NexteraXT DNA sample preparation kit (Illumina) using half the recommended volumes and reagents.
Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies).  Dual-index, single-read sequencing of the pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS Kits (Illumina) with a target depth of 5 million reads per sample.

value: Fibroblasts

value: Skin T cell supernatant

tag: tcellsortforstimulation

tag: tcelldonorid

tag: tcellgmcsf

tag: tcellifngamma

tag: tcelltnfalpha


title: Raji_Mnase-seq_DMSO_2

description:
Treated with DMSO
Raji_Mnase-seq_DMSO_merge_bin10.wig

tag: cell type

tag: cell line

value: DMSO for 2hours

value: DMSO


title: M1524-VE-BS-ES

tag: tissue

value: tissue

value: microglia

tag: genotype

value: Braf VE;CX3 HET

tag: treatment

value: End-stage


title: M1524-VE-Cort-ES

value: brain cortex

value: Braf VE; CX3 HET


title: 1_histio_CEREBELLUM

value: brain

value: Cerebellum

value: Histiocytosis


title: Fib_CD8+CLA+CD103+_PAM126


title: M1521-Ctrl-BS-ES

value: brain brainstem

value: Braf WT;CX3 HET


title: M2617-VE-BS-2mo

value: 2 months


title: Fib_CD4+CLA+CD103+_PAM126


title: RPE_DAY100_P2

city: Bangalore

first: Rajarshi

last: Pal

address: CCAMP, NCBS

country: India

institute: Eyestem research

data_processing:
Adapter Trimming was performed using Trimmomatic (v-0.36)
Contamination removal was performed using Bowtie2 (2.2.4).The unwanted sequences like - mitochondrial genome sequences, ribosomal RNAs, transfer RNAs are removed in this step.
The paired-end reads are aligned to the reference human genome (hg19). Alignment was performed using HISAT2 (2.1.0).
The aligned reads are used for estimating expression of the genes. The raw read counts were estimated using FeatureCount (1.5.2). Read count data were normalized using DESeq2.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include  rawcounts for each Sample

source_name: GMP RPE cells - Enriched and scaled up mature RPE cells suitable for clinical purpose

growth_protocol: Cells were culture in differentiation medium containing specific combination of small molecules and growth factors to promote retinal lineage

extract_protocol:
RNA was isolated from frozen Cell Pellets by TRIzol method
mRNA libraries were prepared for sequencing using NEB Ultra II directional RNA-Seq Library Prep kit (NEB, Cat# E7760L), with Poly-A selection using NEB magnetic Poly(T) beads (NEB, Cat# E7490L)

value: Induced pluripotent stem cells (iPSC)


title: Fib_CD4+CLA+CD103neg_PAM126

value: Fibroblasts


title: Control

city: Grenoble

first: Jérémy

last: LUCAS

address: 17 avenue des Martyrs

institute: CNRS

description: Library alone, no proteins used for this sample. All the DAP-seq steps were still executed  to insure reliabilty of this control.

data_processing:
Alignement to genome is done by Bowtie2
poor quality and multimapped reads are filtered out using samtools
peak-calling is done by MACS2 with parameters (-q 0.001 --call-summits)
Peaks called where Control read coverage is too high are removed from analysis
replicates are treated by MSPC to create consensus peaks
Assembly: Consensus peaks are reworked around maximum of peaks.
Supplementary files format and content: bed format, contains consensus peaks locations of replicates (one per sample, input/control excluded)
Supplementary files format and content: bedgraph format, contains genomic signal values
Library strategy: ampDAP-seq

organism: Arabidopsis thaliana

source_name: 2-weeks old seedlings

growth_protocol: 2-weeks old seedlings of Arabidopsis thaliana

extract_protocol:
Genomic DNA was extracted by chloroform isoamyl alcohol dna extraction protocol
Libraries were contructed using Truseq Illumina kits
Illumina TruSeq adaptors with single end index

value: 2-weeks old seedlings

value: Control


title: Fib_CD8+CLA+CD103neg_PAM120

value: Skin T cell supernatant


title: M1376-VE-BS-ES

value: tissue


title: ARF10

description: Recombinant proteins were produced in bacteria (Rosetta2). Crude extract from bacteria were used.


title: Eyecyte_RPE_split_GLP2

source_name: GLP RPE cells - RPE cells enriched and generated at GLP culture suite


title: Fib_CD8+CLA+CD103+_PAM120


title: For_NGS_OHSU_black_cells_JS

source_name: Research grade RPE cells - RPE cells generated using research grade protocol


title: microglia_App-Psen1_rep1

type: RNA

city: Seville

first: Clara

last: Ortega-de San Luis

address: Av. Manuel Siurot S/N

country: Spain

institute: Instituto de Biomedicina de Sevilla (IBiS); Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Raw data from the extraction software Expression Console was imported to the R statistical processing environment using the LIMMA/Bioconductor package. Quality of the data was assessed using Array Quality Metrics package. Data were normalized using Robust Multi-Array (RMA) method using LIMMA/Bioconductor package.
MTA-1_0 data
MTA-1_0.na34.mm10.transcript.csv

label: Biotin

source_name: Microglia, App-Psen1

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Not applicable

extract_protocol: Brain cortex was isolated from App-Psen1 and Egln3–/–; App-Psen1 mice (12 month-old) and the brain cells were dispersed, labelled with anti-CD11b and CD45 and isolated by FACS. RNA was extracted using TRIZOL.

treatment_protocol: Not applicable


title: microglia_App-Psen1_rep2


title: microglia_Egln3–/–, App-Psen1_rep3

source_name: Microglia, Egln3–/–; App-Psen1

value: Egln3-/-; App-Psen1


title: microglia_Egln3–/–, App-Psen1_rep1


title: microglia_Egln3–/–, App-Psen1_rep2


title: M1375-Ctrl-BS-ES

value: microglia

value: Braf VE; CX3 WT


title: microglia_App-Psen1_rep3


title: M1521-Ctrl-Cort-ES

value: brain cortex

value: Braf WT; CX3 HET

value: End-stage


title: HeLa cells, CRNKL1 siRNA1

city: Dunedin

first: Louise

last: Bicknell

address: 710 Cumberland St

country: New Zealand

institute: University of Otago

description: Library name: CRNKL1_siRNA1

data_processing:
Pre-processing involved adaptor and low-quality trimming (Phred score < Q20) using FASTQ-MCF
The trimmed reads were then mapped against  the human genome sequence GRCh37
Read counts were then retrieved first by exons and summarised per gene using FeatureCount on ENSEMBL gene annotation.
Assembly: human genome sequence GRCh37
Supplementary files format and content: The differential gene expression analysis was performed using DESeq2 package, values listed in a tab-delimited txt file

source_name: HeLa cells

growth_protocol: standard conditions for  HeLa cells

extract_protocol:
RNA extracted using Rneasy kit (Qiagen)
TruSeq stranded Total RNA libraries (Ribo-depletion Gold) as per manufacturers instructions.

value: HeLa cells

value: CRNKL1 knockdown


title: Raji_Mnase-seq_DMSO_1

value: B lymphocyte

tag: strain

value: Burkitt's lymphoma

value: Raji

tag: experiment

value: MNase-Seq

value: DMSO for 2hours

value: DMSO


title: HeLa cells, LacZ siRNA control

description: Library name: HeLa_LacZ

value: WT


title: M1375-Ctrl-Cort-ES


title: M1376-VE-Cort-ES

value: Braf VE; CX3 HET


title: B_05, scTCR-seq

city: Jinan

first: Pinxin

last: Si

state: Shandong

address: Wenhua West Road, Lixia District

institute: Shandong University

description: 10x Genomics

data_processing:
Sequences were aligned to the ensembl human reference transcriptome using the 10x Genomics CellRanger pipeline (version 3.1.0).
Quality control and transcriptome analysis of single-cell datasets were performed using the R package Seurat (version 3.2.0).
Cells were filtered for quality based on the following criteria: mapping to over 200 unique genes and the fraction of unique mitochondrial transcripts was less than 10%.
The TCR library sequences were processed using the CellRanger vdj function supplied with mouse TCR gene annotations and reference sequence files acquired from the International Immunogenetics Information System database (http://www.IMGT.org) and prepared using the mkvdjref function.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files of each sample
Library strategy: scTCR-seq

source_name: peripheral blood

extract_protocol:
Fresh human decidual tissues were washed, cut into small pieces, and then enzymatically dissociated in RPMI 1640 medium (HyClone, Thermo Fisher Scientific, Waltham, MA, USA) containing 1 mg/mL type IV collagenase (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) and 0.01 mg/mL DNase I (Sigma-Aldrich, Louis, MO, USA) at 37 °C with constant agitation for 40 min. The suspensions were filtered through a 70-µm sterile strainer (BD Biosciences, San Jose, CA, USA) using a syringe plunger, washed, and centrifuged on a discontinuous gradient of 20%, 40%, and 60% Percoll bulk for 30 min at 800 g. The DICs were then immediately used for the subsequent cell sorting. Fresh human peripheral blood was collected in K2 EDTA tubes and processed within a few hours. An equal volume of room-temperature phosphate buffered saline (PBS) was mixed with blood and carefully layered over Ficoll Hypaque solution (MP Biomedicals, Santa Ana CA, USA). After centrifugation for 30 min at 2500 rpm (with no break), at room temperature, the mononuclear cell layer was washed three times with excess PBS for 10 min at 1500 rpm and resuspended in 2 ml of PBS. After cell counting, the PBMC samples were immediately allocated for subsequent cell sorting.
Human Tregs (CD45+CD4+CD25hiCD127lo), Tconvs (CD45+CD4+CD25-) and monocytes/macrophages (CD45+CD14+) from decidua and matched peripheral blood were sorted on an Aria Cell Sorter (BD Biosciences). Three types of cells were pooled, counted, and loaded onto a 10x Genomics Chromium Controller instrument for single-cell encapsulation with a 5’VDJ kit (10x Genomics) to recover an estimated 5,000 cells per library. Reverse transcription was performed using a T100TM Thermal Cycler (Bio-Rad) according to the manufacturer’s protocol, followed by the purification of cDNA with silane magnetic beads. Full-length V(D)J segments were enriched via PCR amplification with primers specific to the TCR constant regions. The enriched products were then subjected to Enriched Library Construction. Library quality and concentration were assessed using an Agilent Bioanalyzer 2100. Libraries were run on a Hiseq X or Novaseq for Illumina PE150 sequencing. Due to the unqualified cell viability after FACS-sorting, the decidual Tconvs of P01 and macrophages of P02 were not pooled and examined in the subsequent single-cell sequencing analysis.
single-cell RNA-seq and TCR-seq

value: peripheral blood

value: 20 years old


title: Fib_CD8+CLA+CD103neg_PAM117

value: Fibroblasts

value: Skin T cell supernatant


title: B_07, scTCR-seq

description: 10x Genomics

value: 35 years old


title: B_08, scTCR-seq

description: 10x Genomics

value: 25 years old


title: Fib_CD4+CLA+CD103neg_PAM120


title: Fib_CD4+CLA+CD103+_PAM120


title: HeLa cells, CRNKL1 siRNA2

description: Library name: CRNKL1_siRNA2


title: B_06, scTCR-seq

description: 10x Genomics

value: 21 years old


title: Fib_CD8+CLA+CD103+_PAM117


title: HeLa cells, lipofectamine only control

description: Library name: HeLa_Lipofectamine

value: HeLa cells


title: Adult_RLT_Spleen

city: San Francisco

first: James

last: Gardner

state: CA

address: 505 Parnassus Ave

institute: UCSF

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene aggregation were performed using the Cell Ranger Software (v8.0.1) Downsteam analysis was performed in Python (v3.10.12) using scanpy(v1.10.2) and scVI-tools (v1.1.5).
Assembly: mm10
Supplementary files format and content: h5 file containing raw feature matrix output from Cell Ranger
Supplementary files format and content: h5ad file containing an AnnData object with processed count data. Raw and scVI normalized counts are stored as layers. Cell and gene metadata are stored in the '.obs' and '.var' attribute. UMAP coordinated are stored in the '.obsm' attribute.

source_name: Spleen

extract_protocol:
Mouse spleen, mesenteric, and other lymph nodes (cervical, brachial, axillary, inguinal, and para-aortic) were procured and pooled in digestion medium consisting of RPMI 1640 with 2% foetal bovine serum (FBS) (Sigma-Aldrich), with deoxyribonuclease (DNase) (100 µg/mL; Roche) and LiberaseTM (96 µg/mL; Roche), minced and agitated at 37°C with gentle agitation for 30 min, and passed through a 70-micron filter. Cells were then sorted for live, tdTmt+ MHCII+ cells and processed for single-cell analysis.
10x GEM-X 3' protocol

value: Spleen


title: hESCs, siNAT10, replicate 2

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

description: Library name: siNAT10-2

data_processing:
Clean reads were mapped to mouse genome (UCSC hg19) by using HISAT v2.2.1
Mapped reads were assembled by using Cufflinks v2.2.1
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

source_name: primary human endometrial stromal cells

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
RNA-seq libraries were created by using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: primary human endometrial stromal cells (hESCs) were treated with siNAT10 or siNC for 48h.

value: primary human endometrial stromal cells


title: Adult_RLT_other_LNs

source_name: Other Pooled Lymph Nodes

value: Other Pooled Lymph Nodes


title: B_04, scTCR-seq

description: 10x Genomics

value: 23 years old


title: Adult_RLT_mLN

source_name: Mesenteric Lymph Nodes

value: Mesenteric Lymph Nodes


title: Fib_CD4+CLA+CD103neg_PAM117


title: Fib_CD4+CLA+CD103+_PAM117


title: hESCs, siNAT10, replicate 1

description: Library name: siNAT10-1


title: B_03, scTCR-seq

description: 10x Genomics

value: 22 years old


title: Mm_thymus_B6_P28_Foxn1het_rep4

value: thymus

value: Epcam+CD45- TECs


title: hESCs, siNC, replicate 3

description: Library name: siNC-3


title: B_02, scTCR-seq

description: 10x Genomics


title: Fib_Control_6

value: Conditioned Media

value: Control


title: Mm_thymus_B6_P28_Foxn1het_rep3


title: Fib_CD8+CLA+CD103neg_PAM114


title: B_01, scTCR-seq

description: 10x Genomics

value: peripheral blood

value: 17 years old


title: hESCs, siNC, replicate 2

description: Library name: siNC-2


title: Mm_thymus_B6_P28_Foxn1het_rep2


title: D_08, scTCR-seq

description: 10x Genomics

source_name: deciuda

value: deciuda


title: Fib_CD8+CLA+CD103+_PAM114

value: Fibroblasts

value: Skin T cell supernatant


title: Mm_thymus_B6_P28_Foxn1het_rep1


title: AD ITG brain 28

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: Library name: Sample 28

data_processing:
Raw sequencing reads were aligned to the human genome using HISAT2
Gene counts were obtained using feature Counts from the Subread package v.1.5.2
Assembly: hg38
Supplementary files format and content: tab-delimited text files

source_name: Intermediate 6

extract_protocol:
Total RNA was isolated from eight control and twenty AD ITG brain tissue samples using PureLink RNA Mini Kit (Invitrogen, #12183018A). rRNA depletion using QIAseq® FastSelect™ rRNA HMR kit (Qiagen)
RNA sequencing libraries were constructed at Genewiz (South Plainfield, NJ, USA) with the NEBNext Ultra II RNA Library Preparation Kit for Illumina.

value: Brain

tag: region

value: inferior temporal gyrus

value: Intermediate


title: Fib_CD4+CLA+CD103neg_PAM114


title: Mm_thymus_FVB_P28_WT_rep6

source_name: thymus

value: WT

value: FVB

tag: age


title: D_07, scTCR-seq

description: 10x Genomics

value: 35 years old


title: Fib_CD4+CLA+CD103+_PAM114


title: AD ITG brain 27

description: Library name: Sample 27

source_name: High 8

value: High


title: D_05, scTCR-seq

description: 10x Genomics

value: 20 years old


title: Mm_thymus_FVB_P28_WT_rep5

value: thymus

tag: condition


title: Fib_Control_5

source_name: Fibroblasts


title: AD ITG brain 25

description: Library name: Sample 25

source_name: High 7


title: hESCs, siNAT10, replicate 3

description: Library name: siNAT10-3

value: primary human endometrial stromal cells


title: Mm_thymus_FVB_P28_WT_rep3

value: Epcam+CD45- TECs


title: Fib_CD8+CLA+CD103neg_PAM110


title: D_04, scTCR-seq

description: 10x Genomics

value: 23 years old


title: AD ITG brain 24

description: Library name: Sample 24

source_name: Control 8

value: Control


title: AD ITG brain 23

description: Library name: Sample 23

source_name: Control 7


title: D_03, scTCR-seq

description: 10x Genomics

value: 22 years old


title: Mm_thymus_FVB_P28_WT_rep1


title: D_01, scTCR-seq

description: 10x Genomics

value: deciuda

value: 17 years old


title: AD ITG brain 21

description: Library name: Sample 21

source_name: Control 5


title: Mm_thymus_B6_P28_Ascl1KO_rep3


title: Fib_CD8+CLA+CD103+_PAM110

value: Fibroblasts

value: Skin T cell supernatant


title: hESCs, siNC, replicate 1

description: Library name: siNC-1


title: D_06, scTCR-seq

description: 10x Genomics

value: 21 years old


title: Fib_Control_4

value: Conditioned Media


title: Fib_CD4+CLA+CD103neg_PAM110


title: AD ITG brain 22

description: Library name: Sample 22

source_name: Control 6

value: Brain

value: inferior temporal gyrus


title: B_08, scRNA-seq

description: 10x Genomics

data_processing:
Sequences were aligned to the ensembl human reference transcriptome using the 10x Genomics CellRanger pipeline (version 3.1.0).
Quality control and transcriptome analysis of single-cell datasets were performed using the R package Seurat (version 3.2.0).
Cells were filtered for quality based on the following criteria: mapping to over 200 unique genes and the fraction of unique mitochondrial transcripts was less than 10%.
The TCR library sequences were processed using the CellRanger vdj function supplied with mouse TCR gene annotations and reference sequence files acquired from the International Immunogenetics Information System database (http://www.IMGT.org) and prepared using the mkvdjref function.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files of each sample

value: peripheral blood

value: 25 years old


title: D_02, scTCR-seq

description: 10x Genomics


title: AD ITG brain 20

description: Library name: Sample 20

source_name: Control 4


title: Fib_CD4+CLA+CD103+_PAM110


title: Mm_thymus_FVB_P28_WT_rep2

value: WT

value: FVB


title: AD ITG brain 26

description: Library name: Sample 26

source_name: Intermediate 5

value: Intermediate


title: Fib_CD8+CLA+CD103neg_PAM109


title: Mm_thymus_B6_P28_Ascl1KO_rep2

value: thymus

value: Epcam+CD45- TECs


title: Mm_thymus_B6_P28_Ascl1KO_rep1


title: B_07, scRNA-seq

description: 10x Genomics

source_name: peripheral blood

value: 35 years old


title: Mm_thymus_PWK_P28_WT_rep3

value: PWK


title: Fib_CD4+CLA+CD103neg_PAM109


title: AD ITG brain 19

description: Library name: Sample 19

source_name: Control 3

value: Control


title: Fib_CD8+CLA+CD103+_PAM109


title: Mm_thymus_PWK_P28_WT_rep4


title: B_06, scRNA-seq

description: 10x Genomics


title: AD ITG brain 16

description: Library name: Sample 16

source_name: Intermediate 4


title: Mm_thymus_PWK_P28_WT_rep2


title: B_05, scRNA-seq

description: 10x Genomics

value: 20 years old


title: Mm_thymus_PWK_P28_WT_rep1


title: AD ITG brain 17

description: Library name: Sample 17

source_name: Control 1


title: B_02, scRNA-seq

description: 10x Genomics


title: Fib_CD4+CLA+CD103+_PAM111

value: Fibroblasts

value: Blood T cell supernatant


title: Mammary gland residential macrophage treated with AKT inhibitor in vitro

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

data_processing:
The library pools were denatured and sequenced on Illumina NovaSeq 6000 using the S Prime flowcells as pair-end 65 nt reads according to the manufacturer’s protocol.  Raw sequencing reads were filtered by Illumina NovaSeq Control Software, only the Pass-Filter (PF) reads were de-multiplexed allowing 1 mismatch and used for further analysis.
Demultiplexed raw sequence file (FASTQ) were analyzed using Partek® Flow® software package. Raw reads were aligned using STAR 2.7.8a, followed by quantification to annotation model hg38 – Ensembl Transcripts release 110. After noise filtering, counts were normalized as CPM+1e-4 or FPKM+1.
Assembly: hg38 – Ensembl Transcripts release 110.
Supplementary files format and content: Three processed macrophage data files, i.e Mac_CXCR4+vs-, Mac_cKOs and Mac_invitro are tab delimited text files with value of Log2(CPM+1e-4).
Supplementary files format and content: P4_Ctrl_vs_k8koCxcl12.txt is tab-delimited text file with FPKM value.

source_name: Mammary gland

growth_protocol:
Cell preparation protocol: Single cell suspensions were prepared from the mammary glands of virgin mice using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
Fluorescence-activated cell sorting (FACS) protocol: MaSC enriched P4 population cells are sorted by Lin-CD24+CD29high. Macrophage are sorted by F4/80, CD11b, and further sorted based on CXCR4 expression for CXCR4+ or - subpopulations.
Mammary gland macrophage were prepared and FACS sorted as described above and were cultured in RPMI+2%FBS.

extract_protocol:
Total RNA were extracted using RNeasy mini-prep kit from Qiagen.
The integrity of total RNA samples were assessed on Bioanalyzer 2100 using RNA 6000 Pico chip (Agilent Technologies, CA).  Messenger RNA was enriched from these samples using QIAseq FastSelect - rRNA HMR Kit (Qiagen, CA), fragmented and converted to cDNA and Illumina sequencing library using the PrepX RNA-seq library preparation protocol on the Apollo 324TM NGS Library Prep System (Takara Bio, CA).

treatment_protocol: The macrophage were treated with recombinant CXCL12 and/or AKT inhibitor GSK690693.

value: Mammary gland

value: Macrophage

value: wild type

tag: sorting markers


title: AD ITG brain 13

description: Library name: Sample 13

source_name: High 4

value: Brain

value: inferior temporal gyrus

value: High


title: Mammary gland residential macrophage treated with recombinant Cxcl12 and AKT inhibitor in vitro


title: Fib_CD4+CLA+CD103+_PAM109

value: Skin T cell supernatant


title: B_04, scRNA-seq

description: 10x Genomics

value: peripheral blood

value: 23 years old


title: B_03, scRNA-seq

description: 10x Genomics

value: 22 years old


title: D_08, scRNA-seq

description: 10x Genomics

source_name: deciuda

value: deciuda

value: 25 years old


title: AD ITG brain 15

description: Library name: Sample 15

source_name: High 6


title: Fib_CD4+CLA+CD103+_PAM080


title: Fib_CD4+CLA+Th1/17_PAM080


title: AD ITG brain 14

description: Library name: Sample 14

source_name: High 5


title: Mammary gland residential macrophage treated with recombinant Cxcl12 in vitro


title: Mm_thymus_FVB_P28_WT_rep4

source_name: thymus

value: thymus

value: Epcam+CD45- TECs

value: WT

value: FVB


title: Fib_CD4+CLA+Th17_PAM111

source_name: Fibroblasts

value: Fibroblasts

value: Blood T cell supernatant


title: AD ITG brain 12

description: Library name: Sample 12

source_name: High 3


title: AD ITG brain 18

description: Library name: Sample 18

source_name: Control 2

value: Control


title: AD ITG brain 11

description: Library name: Sample 11

source_name: Low 6

value: Low


title: D_06, scRNA-seq

description: 10x Genomics

value: 21 years old


title: Fib_CD4+CLA+Th1/17_PAM081


title: Mammary gland residential macrophage from mice with Cxcl12 KO in luminal cells by K8-cre, repeat 2

value: Mammary gland

value: Macrophage

value: K8Cre+, Cxcl12fl/fl


title: AD ITG brain 10

description: Library name: Sample 10

source_name: Low 5

value: Brain

value: inferior temporal gyrus


title: B_01, scRNA-seq

description: 10x Genomics

value: peripheral blood

value: 17 years old


title: AD ITG brain 9

description: Library name: Sample 9

source_name: Low 4


title: AD ITG brain 7

description: Library name: Sample 7

source_name: Intermediate 2

value: Intermediate


title: D_04, scRNA-seq

description: 10x Genomics

value: deciuda

value: 23 years old


title: D_07, scRNA-seq

description: 10x Genomics

value: 35 years old


title: Mammary gland residential macrophage cultured in vitro

value: wild type


title: Fib_CD4+CLA+Th1_PAM111

value: Fibroblasts


title: Mammary gland residential macrophage from K8-cre wild type control mice, repeat 1


title: AD ITG brain 6

description: Library name: Sample 6

source_name: High 2

value: High


title: AD ITG brain 8

description: Library name: Sample 8

source_name: Intermediate 3


title: Fib_CD4+CLA+Th17_PAM108

value: Blood T cell supernatant


title: Mammary gland residential macrophage from mice with Cxcl12 KO in luminal cells by K8-cre, repeat 1


title: D_05, scRNA-seq

description: 10x Genomics

value: 20 years old


title: Fib_CD4+CLA+CD103+_PAM108


title: Fib_CD4+CLA+Th22_PAM111


title: Mammary gland residential macrophage from K8-cre wild type control mice, repeat 2


title: MaSC enriched subpopulation P4 (Lin-CD24+CD29high) from mice with Cxcl12 cKO in luminal cells by K8-cre

value: MaSC enriched basal cell


title: D_02, scRNA-seq

description: 10x Genomics

value: 21 years old


title: D_01, scRNA-seq

description: 10x Genomics


title: AD ITG brain 5

description: Library name: Sample 5

source_name: High 1


title: Fib_CD4+CLA+Th2_PAM108


title: MaSC enriched subpopulation P4 (Lin-CD24+CD29high) from wild type mice

value: Mammary gland


title: CCK81_MYB

first: Fuyuan

last: Li

address: No. 2005, Songhu Road, Xinjiangwancheng Street, Yangpu District

department: School of life science

institute: Fudan University

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie version 2.2.5. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.2.6 with the significance cut-off q-value <=0.01
BedGraph files were generated by MACS2, sorted, and normalized by the mean genome-wide bedGraph signal in each dataset. Bigwig tracks were generated from bedGraph using UCSC tool bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: DMEM, 10% fetal bovine serum,  1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using a sonicator (QSonica Q800R3).
ChIP-seq libraries were prepared using the TruSeq ChIP Library Preparation Kit according to the User Guide Documentation. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Colorectal Adenocarcinoma

tag: chip antibody

value: MYB (Abcam, #ab45150)


title: SNU719_MYB


title: Fib_CD4+CLA+Th1_PAM108

tag: tcellsortforstimulation


title: Fib_Control_3

value: Conditioned Media

value: Control

tag: tcelldonorid


title: Mammary gland residential macrophage subpopulation with Cxcr4+, repeat 1

value: Macrophage, CXCR4+


title: D_03, scRNA-seq

description: 10x Genomics

value: 22 years old


title: HT55_MYB


title: Fib_CD4+CLA+CD103+_PAM107

tag: tcellgmcsf


title: Mammary gland residential macrophage subpopulation with Cxcr4+, repeat 2


title: AD ITG brain 3

description: Library name: Sample 3

source_name: Low 3

value: Brain

value: inferior temporal gyrus

value: Low


title: Fib_CD4+CLA+Th22_PAM107

tag: tcellifngamma


title: Mammary gland residential macrophage with Cxcr4 KO by Lysm-Cre, repeat 2

source_name: Mammary gland

value: Macrophage

value: LysmCre+, Cxcr4fl/fl


title: AD ITG brain 1

description: Library name: Sample 1

source_name: Low 1


title: AD ITG brain 4

description: Library name: Sample 4

source_name: Intermediate 1

value: Intermediate


title: Fib_CD4+CLA+Th17_PAM107

value: Fibroblasts

value: Blood T cell supernatant

tag: tcelltnfalpha


title: hum8h3B5 QSP

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15
Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artefact reads (all but three bases in the read equal one base type) were filtered using FastX 0.0.14 and ShortRead 1.40.0
With Bowtie2 2.3.3.1 we identified and removed reads that aligned to phix_illumina
The pre-processed reads were aligned with STAR aligner v2.5.2b to the reference genome of Homo sapiens (GRCh38.88) or Mus musculus (GRCm38.82) . Default STAR aligner parameter settings were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments
The number of reads in the alignments that overlap with gene features were counted with featureCounts 1.5.3. Following parameters were chosen: -Q 0 -s 2 -t exon -g gene_id. We removed genes for which all samples had less than 1 count-per-million. Raw counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor
Assembly: Homo sapiens (GRCh38.88) or Mus musculus (GRCm38.82)
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample for each mapped genome.

source_name: human quadriceps muscle

growth_protocol: C2C12 myoblasts were cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% foetal bovine serum, 100 units/mL penicillin, and 100 μg/mL streptomycin. For differentiation of the C2C12 myoblasts into myotubes, proliferation medium was replaced by differentiation medium when cells reached 80% confluence. Differentiation medium consisted of DMEM supplemented with 2% horse serum and 1% Pen/Strep. Human myoblasts were cultured in Skeletal Muscle Cell Media (PromoCell, no. C-23060), supplemented with 10% FBS and 1% Pen/Strep. For differentiation, proliferation medium was replaced by differentiation medium when cells reached 80% confluency (DMEM glutamax with 2% horse serum and 1% Pen/Strep).

extract_protocol:
Cells were scraped off from the well surface and resuspended in RLT lysis buffer (Qiagen). Total RNA was extracted from these lysed cells using RNeasy micro columns (Qiagen).
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-8000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 or Fragment Analyzer (Agilent). Per sample, an amount of 100 ng of total RNA was used as input. Using the Illumina TruSeq(r) Stranded mRNA Sample Prep Kit (protocol version: Part # 1000000040498 v00 October 2017) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence-libraries of each sample were equimolarly pooled and sequenced on Illumina NovaSeq 6000 (S1 flowcell 100 cycles kit v1.5, 100 bp, Single Reads) at the VIB Nucleomics core (www.nucleomics.be).

treatment_protocol: Murine (C2C12) or human (AB678C53Q) myotubes were treated with quorum sensing peptide iAM373 or placebo for 8 hours or 24 hours.

value: QSP

tag: incubation time


title: Fib_CD4+CLA+Th1/17_PAM107

tag: cell type


title: Mammary gland residential macrophage subpopulation with negative Cxcr4

tag: tissue

value: Macrophage, CXCR4-

value: wild type


title: hum8h3B4 Placebo

value: Placebo


title: Mammary gland residential macrophage from Lysm-cre wild type control mice, repeat 2

value: Mammary gland

tag: genotype

value: LysmCre+


title: hum8h3C3 Placebo

tag: treatment


title: ND_GMP_1

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

data_processing:
Raw paired-end reads quality control was determined using FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
read trimming was performed using Trim Galore software (https://doi.org/10.5281/zenodo.5127899) to remove residual adapters and low-quality sequences.
Trimmed reads were aligned against the human reference genome (GRCh38) using STAR with standard input parameters and only uniquely mapped reads were considered for downstream analyses.
Reads were assigned to genes with the featureCounts tool using the GENCODE primary assembly v.35 gene transfer file (GTF) as reference annotation for the genomic features.
Gene count matrices were then processed by the R/Bioconductor differential gene expression analysis packages DESeq2 (37) following standard workflows.
Assembly: GENCODE primary assembly v.35 gene transfer file (GTF)
Supplementary files format and content: Raw read counts

source_name: Bone marrow

extract_protocol:
RNA was extracted by using RNA microkit (Qiagen). 1 ng of RNA has been used for library preparation as input.
Ovation SoLo RNA-seq kit’ (NuGEN, San Carlos, CA) has been used for library preparation following the manufacturer’s instructions.

value: GMPs

tag: disease

value: Healthy

value: Bone marrow


title: ND_GMP_2


title: Mammary gland residential macrophage with Cxcr4 KO by Lysm-Cre, repeat 1


title: Fib_CD4+CLA+Th2_PAM107


title: Mammary gland residential macrophage from Lysm-cre wild type control mice, repeat 1


title: ND_CMP_2

value: CMP CD71+BAH1+/-


title: ND_CMP_1


title: hum8h2C4 QSP


title: hum8h2C3 Placebo


title: Dnmt3a 22

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: 10X Genomics

data_processing:
Illumina base call files for all libraries were demultiplexed and converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina).
A filtered digital gene expression matrix was generated for each single cell gene expression library against the 10X Genomics mm10 reference build (version 2020-A, GRCm38 assembly with GENCODE M23 annotations) using 10X Genomics CellRanger count version6.0.0for all samples.
For all single cell samples, R1 contains a 16bp cell barcode + 12bp UMI barcode. For all samples, R2 contains a 91bp biological read.
The resultant counts matrices were input into PartekFlow for downstream analysis and visualization.
Assembly: mm10

extract_protocol:
Single cell suspensions from each mouse were prepared by crushing spines, sternums, humeri, tibias, femurs, and iliac crests.  Niche cells were submitted to enzymatic digest, stained, and sorted on a FACSympony S6 sorter. Hematopoietic cells pass through a ficoll gradient, stained, and sorted on a FACSAria II sorter.
The cells were immediately processed as follows. Cells were counted on a Countess II automated cell counter (ThermoFisher), and 12,000 cells were loaded into one lane of a 10X Chromium microfluidic chip. Single cell capture, barcoding and library preparation were performed using the 10X Chromium version 3.1 NEXTGEM chemistry, according to the manufacturer’s protocol (#CG000315). cDNA and libraries were checked for quality on Agilent 4200 Tapestation and quantified by KAPA qPCR before sequencing. each gene expression library was sequenced at 18.75% of an Illumina NovaSeq 6000 S4 flow cell lane, targeting 6,000 barcoded cells with an average sequencing depth of 75,000 reads per cell.

value: hematopoietic and niche cells


title: Fib_CD4+CLA+Th22_PAM106


title: Fib_CD4+CLA+Th1_PAM107


title: Fgd5 36

description: 10X Genomics


title: Fib_CD4+CLA+CD103+_PAM106


title: hum8h2C2 QSP


title: ND_MEP_2

value: MEPs CD71+BAH1+/-


title: AD ITG brain 2

city: New York

description: Library name: Sample 2

source_name: Low 2

value: Brain

value: inferior temporal gyrus

value: Low


title: Fib_CD4+CLA+Th17_PAM106

source_name: Fibroblasts

value: Fibroblasts


title: ND_MPP_2

value: MPPs


title: Dnmt3a 21

description: 10X Genomics


title: ND_MPP_1


title: Dnmt3a 20

description: 10X Genomics


title: Fgd5 15

description: 10X Genomics


title: hum8h2B5 QSP

value: QSP


title: Fib_CD4+CLA+Th1/17_PAM106

value: Blood T cell supernatant


title: hum8h3B3 QSP


title: hum8h2B4 Placebo


title: ND_HSC_2

value: HSCs


title: hum8h2B3 QSP


title: Fib_CD4+CLA+Th2_PAM106


title: Fgd5 13

description: 10X Genomics


title: hum8h2C5 Placebo

value: Placebo


title: ND_MEP_1


title: hum8h2B2 Placebo


title: Fib_CD4+CLA+Th1_PAM106


title: Fib_CD4+CLA+CD103+_PAM105


title: hum8h1C5 Placebo


title: ND_HSC_1


title: Fgd5 12

description: 10X Genomics


title: Fib_Control_2

value: Conditioned Media

value: Control


title: mur8h3C4 QSP

source_name: C2C12 murine muscle


title: mur8h3C5 Placebo


title: TAL_CMP_1

value: Thalassemia


title: TAL_GMP_1

value: GMPs


title: TAL_GMP_2

value: Bone marrow


title: mur8h3C3 Placebo


title: hum8h1C2 QSP


title: mur8h3C2 QSP


title: TAL_MEP_2


title: mur8h3B5 QSP


title: Fib_CD4+CLA+Th22_PAM105


title: TAL_CMP_2

value: CMP CD71+BAH1+/-


title: hum8h1B4 Placebo


title: Fib_CD4+CLA+Th1/17_PAM105


title: Fib_CD4+CLA+Th2_PAM105


title: hum8h1B5 QSP


title: mur8h3B4 Placebo


title: TAL_MPP_2


title: Dnmt3a 18

description: 10X Genomics

value: hematopoietic and niche cells


title: Fib_CD4+CLA+Th1_PAM105


title: hum8h1B3 QSP


title: hum8h1B2 Placebo


title: Fib_Control_1


title: Fib_CD4+CLA+Th22_PAM104


title: mur8h3B2 Placebo


title: hum24h3C4 QSP


title: hum8h1C4 QSP


title: mur8h3B3 QSP


title: TAL_HSC_1


title: Fib_CD4+CLA+Th17_PAM105


title: hum24h3C3 Placebo


title: Fib_CD4+CLA+Th17_PAM104


title: HT55 cells, shMYB rep3

city: Shanghai

data_processing:
Paired-end reads were trimmed for adaptor sequence and masked for low-quality sequences, then were aligned to mouse genome (hg10) using STAR version 2.7.10
Uniquely mapped reads were quantified with HTSeq.
Protein-coding genes with more than 1 read count in at least two samples (n = 20138) were included for downstream analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

growth_protocol: HT55 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% P/S in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Zymo Quick-RNA miniprep kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kit t following manufacturer's protocols.

tag: cell line

value: Colorectal Adenocarcinoma

value: MYB knockdown


title: Fib_CD4+CLA+Th2_PAM104


title: TAL_MEP_1

value: MEPs CD71+BAH1+/-


title: hum24h3C2 QSP


title: mur8h2C2 QSP


title: mur8h2C3 Placebo


title: HT55 cells, shMYB rep2


title: mur8h2B3 QSP


title: HT55 cells, shMYB rep1


title: Fib_CD4+CLA+Th1_PAM104


title: hum24h3B4 Placebo


title: TAL_HSC_2


title: TAL_MPP_1


title: hum24h3B5 QSP


title: mur8h2B2 Placebo


title: HT55 cells, shControl rep3

value: WT


title: Fib_CD4+CLA+CD103+_PAM096

value: Fibroblasts


title: mur8h1C4 QSP


title: Fib_Control_0


title: HT55 cells, shControl rep2


title: Fib_CD4+CLA+Th22_PAM096


title: hum24h3B3 QSP


title: Fib_CD4+CLA+Th17_PAM096


title: mur8h1C5 Placebo


title: mur8h1C3 Placebo


title: hum24h2C5 Placebo


title: HT55 cells, shControl rep1


title: Fib_CD4+CLA+Th2_PAM096


title: Fib_CD4+CLA+Th1_PAM096


title: mur8h1C2 QSP


title: Control_NoDrug_Lung_26

city: Aurora

first: Christopher

middle: Andrew

last: Mancuso

state: CO

address: 13001 East 17th Place

department: Department of Biostatistics and Informatics

institute: University of Colorado Anschutz Medical Campus

description:
Library name: Sample_95
Control_M_Lung_26

data_processing:
Raw sequencing reads were de- multiplexed using bcl2fastq. The de-multiplexed fastq files were aligned using the Nextflow based nf-core rnaseq pipeline utilizing Singularity containers. Through this pipeline, Illumina adaptor sequences and low-quality sequencing bases were removed from the fastq files using the TrimGalore! implementation of cutadapt. The resulting reads were aligned to the Sus Scrofa genome using STAR and quantified using Salmon. Comprehensive quality control of every step of the pipeline was performed using MultiQC.
Assembly: Sscrofa11.1
Supplementary files format and content: Count file generated by the nf-core pipeline. Rows are genes and columns are samples.

organism: Sus scrofa

source_name: Lung

growth_protocol: Infant swine between 5 – 10 kg

extract_protocol:
Kidney and terminal ileum were harvested en bloc immediately prior to euthanasia while liver, heart, and lungs were harvested immediately following euthanasia to allow circulation of the pentobarbital. All organs underwent passive venous drainage prior to processing and storage. Tissue samples were flash-frozen in liquid nitrogen and stored at −80◦C until homogenized and used for total RNA isolation from kidney (cortex), liver, heart (left ventricle), lungs (right lower lobe), and ileum with the RNeasy Plus Mini Kit (Qiagen, Santa Clarita, CA, USA) as described in the manufacturer’s protocol. RNA concentrations were quantified at 260 nm, and the purity and integrity were determined using NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA).
Samples underwent whole transcriptome RNA sequencing at the University of Colorado Genomics Shared Resource (Aurora, CO, USA). RNA purity, quantity and integrity were determined with NanoDrop and TapeStation 4200 (Agilent Technologies, Santa Clara, CA, USA) analysis prior to RNA-seq library preparation. The Universal Plus mRNA-Seq library preparation kit with NuQuant was used (Tecan, Morrisville, NC, USA) with an input of 200 ng of total RNA to generate RNA-Seq libraries. Paired-end sequencing reads of 150 bp were generated on NovaSeq 6000 sequencer (Illumina, San Diego, CA, USA) at a target depth of 80 million paired-end reads per sample.

value: Lung

tag: intervention

value: NoDrug

tag: Sex

value: M

tag: animal id

tag: batch


title: hum24h2C3 Placebo


title: hum24h2C4 QSP

value: QSP


title: Ker_CD8+CLA+CD103neg_PAM126

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: Keratinocytes

value: Keratinocytes

value: Skin T cell supernatant


title: mur8h1B5 QSP


title: CPB_Lind_Lung_24

description:
Library name: Sample_93
CPB_Lind_Lung_24

value: CPB/DHCA

value: Linrodostat


title: CPB_NoDrug_Lung_25

description:
Library name: Sample_94
CPB_Lung_25


title: hum24h2B4 Placebo

value: Placebo


title: mur8h1B3 QSP


title: hum24h3B2 Placebo


title: mur8h1B4 Placebo


title: CPB_NoDrug_Lung_21

description:
Library name: Sample_92
CPB_Lung_21

value: F


title: Ker_CD4+CLA+CD103neg_PAM126


title: Ker_CD8+CLA+CD103+_PAM126


title: CPB_Lind_Lung_20

description:
Library name: Sample_91
CPB_Lind_Lung_20


title: mur24h3B5 QSP


title: hum24h1C5 Placebo


title: hum24h1C4 QSP


title: Ker_CD8+CLA+CD103neg_PAM120


title: Ker_CD4+CLA+CD103+_PAM126


title: CPB_NoDrug_Lung_19

description:
Library name: Sample_90
CPB_Lung_19


title: mur24h3B4 Placebo


title: Ker_CD8+CLA+CD103+_PAM120


title: mur24h3B3 QSP


title: hum24h1C3 Placebo


title: CPB_Lind_Lung_18

description:
Library name: Sample_89
CPB_Lind_Lung_18


title: Control_NoDrug_Lung_15

description:
Library name: Sample_88
Control_F_Lung_15

value: Control


title: hum24h1C2 QSP


title: Control_NoDrug_Lung_14

description:
Library name: Sample_87
Control_F_Lung_14


title: mur24h3B2 Placebo


title: hum24h1B5 QSP


title: Fib_CD4+CLA+Th22_PAM108

value: Blood T cell supernatant


title: Ker_CD4+CLA+CD103neg_PAM120


title: hum24h2B3 QSP


title: mur8h1B2 Placebo


title: mur24h2C5 Placebo


title: hum24h1B4 Placebo


title: CPB_Lind_Lung_12

description:
Library name: Sample_85
CPB_Lind_Lung_12


title: Ker_CD8+CLA+CD103neg_PAM117


title: mur24h2C4 QSP


title: hum24h1B3 QSP


title: CPB_NoDrug_Lung_11

description:
Library name: Sample_84
CPB_Lung_11


title: mur24h2C3 Placebo


title: Control_NoDrug_Lung_10

description:
Library name: Sample_83
Control_M_Lung_10


title: Ker_CD4+CLA+CD103neg_PAM117


title: hum24h1B2 Placebo


title: mur24h2C2 QSP


title: mur24h2B5 QSP


title: Raji_chrRNA-seq_T10_PDS_rep2_3

city: Montpellier

first: Amal

last: Makrini

address: 1919 route de mende

institute: IGMM

description:
Raji_PDS_chRNA_10min_neg.wig
Raji_PDS_chRNA_10min_pos.wig

data_processing:
Mnase-seq  and ChIP-seq samples were aligned to human genome (hg19, GRCh37) using Bowtie 2 aligner. Samples were then treated using PASHA pipeline to produce wig files (Fenouil et al. 2016). Uniquely aligned tags were elongated after estimating optimal elongation size in silico for single ended sequencing or between the pairs for paired end sequencing, enabling to use the original fragment length for further processing. Signals were scaled according to the mean signal. The number of tags covering each nucleotide of the genome was computed and averaged in bins of 10 or 50 nucleotides. For MNase-seq datasets, signals were smoothed on 5 bins.
RNA-seq samples were aligned to human genome (hg19, GRCh37)  and ERCC  reference using tophat2 aligner.
Genome_build: hg19
Supplementary_files_format_and_content: wig

source_name: Raji B cells

growth_protocol: Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/mL) and glutamin (2 mg/ml) at 37°C and 5% CO2.

extract_protocol:
Fifty million cells were used to perform each Pol II ChIP-seq experiments. Cells were crosslinked for 10 min at 20°C with the crosslinking solution (10 mM NaCl, 0.1 mM EDTA pH 8, 0.05 mM EGTA pH 8, 5 mM HEPES pH 7.8 and 1% formaldehyde). The reaction was stopped by adding glycine at a final concentration of 250 mM. After 5 min of formaldehyde quenching, cells were washed twice with cold PBS and resuspended in cold 2.5L LB1 (50 mM HEPES pH 7.5, 140 mM NaCl,1 mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) at 4°C for 20 min on a rotating wheel. Nuclei were pelleted down by spinning at 1350 rcf in a refrigerated centrifuge and washed in 2.5L LB2 (200 mM NaCl, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, 10 mM Tris pH 8) for 10 min at 4°C on a rotating wheel followed by centrifugation to collect nuclei. Nuclei were then resuspended in 1L LB3 (1 mM EDTA pH 8, 0.5 mM EGTA pH8, 10 mM Tris pH8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using Bioruptor Pico (Diagenode) in 15L tubes for 20 cycles of 30 s ON and 30 s OFF pulses in 4°C bath. All buffers (LB1, LB2 and LB3) were complemented with EDTA free Protease inhibitor cocktail (Roche), 0.2 mM PMSF and 1 µg/L Pepstatin just before use. After sonication, Triton X-100 was added to a final concentration of 1% followed by centrifugation at 20000 rcf and 4°C for 10 min to remove particulate matter. For sequencing of nucleosomal DNA in Raji cells, 35x106 cells were resuspended in 350μl Solution I (150 mM sucrose, 80 mM KCl, 5 mM K2HPO4, 5 mM MgCl2, 0.5 mM CaCl2, 35 mM HEPES pH 7.4) and NP40 was added to a final concentration of 0.2%. Cell membranes were permeabilized for five min at 37°C. MNase was prepared at 50, 25, 12, 6 or 3 units in 0.5L of Solution II (150 mM sucrose, 50 mM Tris pH 8, 50 mM NaCl, 2 mM CaCl2) and incubated with 50 µL of cellular preparation, corresponding to 5.106 cells, for exactly 10 min at 37°C. The reactions were stopped by adding of EDTA to a final concentration of 10 mM. The cells were lysed using 1.45L of SDS Lysis Buffer (1% SDS, 10 mM EDTA pH 8, 50 mM Tris pH 8), with 10 min incubation at 4°C. 200μl aliquots were taken for purification and the remaining extracts were stored at -80°C. An equal volume of TE (200ul) was added to the aliquots, followed by subsequent 2 hour treatments with each 0.2µg/L final concentrations of RNase A and Proteinase K at 37°C and 55°C, respectively. DNA was extracted by two subsequent phenol:chloroform:isoamylalcohol (25:24:1) extractions, further purified using QIAquick PCR purifications colums (Qiagen, Germany). Nucleosomal digestion was verified by running 500ng of DNA on a 1.5% agarose gel as well as on DNA high-sensitivity 2100 Bioanalyzer chips (Agilent, USA). Digestions showing 75% of mononucleomes (running at 150bp) were selected for library preparations.  Chromatin RNA fraction was prepared from ∼20x10^6 Raji cells. Cells were washed with ice-cold PBS twice. The cells were lysed with ice-cold 4 ml of HLB/NP40 buffer (10 mM Tris-Hcl, pH 7.5, 10 mM NaCl, 0.5% NP40, and 2.5 mM MgCl2) and incubated on ice for 5 min. After the incubation, 1 ml of ice-cold HLB/NP40/Sucrose buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP40, 2.5 mM MgCl2, and 10% Sucrose) was under-laid and then the nuclei were collected under 1,400 rcf centrifuge at 4°C for 5 min. Isolated nuclei were resuspended in 125 μl of NUN1 solution (20 mM Tri-HCl, pH 8.0, 75mM NaCl, 0.5 mM EDTA, 50% Glycerol) followed by 1.2 ml NUN2 buffer (20 mM HEPES-KOH pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% NP40). Fifteen minute incubation was carried out on ice with mixing by max speed vortex for 5 s every ∼4 min and then chromatin pellets were precipitatd under 15,000 rcf centrifuge at 4°C for 10 min. Chromatin pellet was resuspended in 500 μl NUN2 buffer. Chromatin were precipitated under 15,000 rcf centrifuge at 4°C for 10 min, then Chromatin RNAs were extracted by 500 μl of Trizol reagent (Life technologies). The RNA extraction steps were repeated three times with rigorous treatment with TurboDNase in beetween.
Mnase-seq and ChIP-seq librairies were prepared using Illumina's ChIP Sample Prep Kit according to standard protocol.  ChrRNA-seq librairies were prepared using Illuminas's "TruSeq® Stranded Total RNA Library Prep Gold (ref. 20020599)" kit according to standard protocol.

treatment_protocol: For the α-amanitin experiments, cells were treated with 2.5 µg/mL at the indicated times. For the Pyridostatin experiments, cells were treated with 10 µM pyridistatin

value: B lymphocyte

tag: strain

value: Burkitt's lymphoma

value: Raji

tag: experiment

value: RNA-seq

tag: spike-in cell line

value: ERCC

tag: chip antibody

value: ChrRNA

value: 10 microM Pyridostatin

tag: time point

value: 10 minutes


title: CPB_NoDrug_Lung_9

description:
Library name: Sample_82
CPB_Lung_9

value: Lung

value: NoDrug

value: M


title: Ker_Control_6

extract_protocol:
High-quality total RNA was isolated from approximately 2 x 104 T cell supernatant-treated keratinocytes or fibroblasts using TRIzolTM Reagent (InvitrogenTM; 15596026). cDNA was prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara).
Library construction was performed using the NexteraXT DNA sample preparation kit (Illumina) using half the recommended volumes and reagents.
Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies).  Dual-index, single-read sequencing of the pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS Kits (Illumina) with a target depth of 5 million reads per sample.

value: Keratinocytes

value: Conditioned Media

tag: tcellsortforstimulation

tag: tcelldonorid

tag: tcellgmcsf

tag: tcellifngamma

tag: tcelltnfalpha


title: Ker_CD4+CLA+CD103+_PAM120

tag: cell type

tag: treatment

value: Skin T cell supernatant


title: Control_NoDrug_Lung_7

description:
Library name: Sample_81
Control_M_Lung_7

tag: tissue


title: mur24h2B4 Placebo

value: Placebo

tag: incubation time


title: CPB_NoDrug_Lung_6

description:
Library name: Sample_80
CPB_Lung_6

tag: intervention

value: CPB/DHCA

tag: Sex

value: F


title: mur24h2B3 QSP

value: QSP


title: Control_NoDrug_Lung_13

description:
Library name: Sample_86
Control_F_Lung_13

value: Control

tag: animal id

tag: batch


title: Raji_chrRNA-seq_T10_PDS_rep2_1

value: B lymphocyte

tag: strain

value: Burkitt's lymphoma

tag: cell line

value: Raji

tag: experiment


title: Ker_CD8+CLA+CD103neg_PAM114


title: Raji_chrRNA-seq_T10_PDS_rep2_2

value: RNA-seq

tag: spike-in cell line

value: ERCC

tag: chip antibody

value: ChrRNA

tag: time point


title: Ker_CD8+CLA+CD103+_PAM114

tag: tcellsortforstimulation

tag: tcelldonorid

tag: tcellgmcsf


title: Ker_CD8+CLA+CD103+_PAM117

tag: cell type

tag: tcellifngamma

tag: tcelltnfalpha


title: Control_NoDrug_Lung_4

description:
Library name: Sample_79
Control_F_Lung_4

tag: tissue

value: Lung

tag: treatment


title: Raji_chrRNA-seq_T10_PDS_rep1_4

value: 10 microM Pyridostatin

value: 10 minutes


title: mur24h2B2 Placebo

tag: incubation time


title: CPB_NoDrug_Lung_2

description:
Library name: Sample_78
CPB_Lung_2

tag: intervention

value: NoDrug

tag: Sex

value: M

tag: animal id


title: Ker_CD4+CLA+CD103neg_PAM114

value: Keratinocytes

value: Skin T cell supernatant


title: Raji_chrRNA-seq_T10_PDS_rep1_3

tag: strain

tag: cell line


title: Raji_chrRNA-seq_T10_PDS_rep2_4

tag: experiment

tag: spike-in cell line


title: Raji_chrRNA-seq_T10_PDS_rep1_2

tag: chip antibody

tag: time point


title: Control_NoDrug_Lung_1

description:
Library name: Sample_77
Control_M_Lung_1

tag: batch


title: mur24h1C4 QSP


title: mur24h1C5 Placebo

value: Placebo


title: Ker_CD4+CLA+CD103+_PAM114

tag: tcellsortforstimulation

tag: tcelldonorid

tag: tcellgmcsf


title: Ker_CD4+CLA+CD103+_PAM117

tag: cell type

tag: tcellifngamma

tag: tcelltnfalpha


title: Ker_Control_5

tag: treatment

value: Conditioned Media


title: Control_NoDrug_Liver_26

description:
Library name: Sample_76
Control_M_Liver_26

source_name: Liver

tag: tissue

value: Liver

tag: intervention


title: mur24h1C3 Placebo

tag: incubation time


title: Ker_CD8+CLA+CD103neg_PAM110


title: mur24h1C2 QSP

value: QSP


title: Raji_chrRNA-seq_T10_PDS_rep1_1

value: B lymphocyte

tag: strain


title: CPB_Lind_Liver_24

description:
Library name: Sample_74
CPB_Lind_Liver_24

value: CPB/DHCA

value: Linrodostat

tag: Sex

tag: animal id


title: CPB_NoDrug_Liver_25

description:
Library name: Sample_75
CPB_Liver_25


title: Ker_CD4+CLA+CD103neg_PAM110


title: mur24h1B5 QSP


title: Raji_chrRNA-seq_T0_PDS_rep2_3

description:
Raji_PDS_chRNA_0min_neg.wig
Raji_PDS_chRNA_0min_pos.wig

value: Burkitt's lymphoma

tag: cell line

value: Raji

tag: experiment

value: RNA-seq

tag: spike-in cell line

value: untreated


title: Ker_CD8+CLA+CD103+_PAM110


title: mur24h1B4 Placebo


title: Raji_chrRNA-seq_T0_PDS_rep2_2

value: ERCC

tag: chip antibody

value: ChrRNA

tag: time point


title: Ker_CD4+CLA+CD103+_PAM110

tag: tcellsortforstimulation

tag: tcelldonorid


title: Raji_chrRNA-seq_T0_PDS_rep2_4

tag: cell type


title: Raji_chrRNA-seq_T0_PDS_rep2_1


title: CPB_NoDrug_Liver_21

description:
Library name: Sample_73
CPB_Liver_21

value: NoDrug

value: F

tag: batch


title: CPB_Lind_Liver_20

description:
Library name: Sample_72
CPB_Lind_Liver_20


title: Ker_Control_4

value: Keratinocytes

value: Control

tag: tcellgmcsf

tag: tcellifngamma

tag: tcelltnfalpha


title: mur24h1B2 Placebo

tag: treatment

value: Placebo


title: CPB_NoDrug_Liver_19

description:
Library name: Sample_71
CPB_Liver_19

tag: tissue

tag: intervention


title: Raji_chrRNA-seq_T0_PDS_rep1_4

tag: strain


title: Raji_chrRNA-seq_T0_PDS_rep1_3


title: Ker_CD4+CLA+CD103+_PAM080

value: Blood T cell supernatant


title: CPB_Lind_Liver_18

description:
Library name: Sample_70
CPB_Lind_Liver_18

value: Liver

tag: Sex

tag: animal id


title: Control_NoDrug_Liver_15

description:
Library name: Sample_69
Control_F_Liver_15


title: Pachon_new_starved_1

city: Kansas City

first: Di

last: Wu

institute: Stowers Institute for Medical Research

description:
Library name: L66828
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_new_starved_1

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl-convert 3.10.5 Reads were aligned to UCSC genome Astyanax_mexicanus-2.0 with STAR aligner (version 2.7.10b), using Ens_110 gene models. TPM values were generated using RSEM (version v1.3.1).
Assembly: Astyanax_mexicanus-2.0 (Annotation: Ensembl 110)
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample
Supplementary files format and content: tab-delimited txt file includes cpm for each sample

organism: Astyanax mexicanus

source_name: Ovary

extract_protocol:
Total RNA was extracted using standard phenol/chloroform extraction. 1 ml of Trizol (15596026, Thermo Fisher Scientific) was used per 50 to 100 mg tissue. Samples were homogenized with Trizol and 3.0 mm TriplePure M-Bio Grade beads (D1132-30, Benchmark Scientific) on Beadbug 6 homogenizer (D1036, Benchmark Scientific). After a brief centrifugation, 200 µl of chloroform was added per 1 ml of Trizol, then vortex for 15 seconds and incubated at room temperature for 2 min. Samples were centrifuged at 12,000 g for 15 min at 4°C. Upper transparent aqueous phase was transferred carefully without disturbing the interphase into fresh tube and added with 500 µl of Isopropyl alcohol per 1 ml of Trizol used initially. 2 µl of GlycoBlue Coprecipitant (AM9515, Thermo Fisher Scientific) was added to visualize RNA pellets. Samples were incubated at room temperature for 10 min and centrifuged at 12,000 g for 10 min at 4°C. Supernatant was removed and RNA pellets were washed twice with 1 ml of 75% ethanol per 1 ml Trizol used initially. Samples were mixed by vortexing and centrifuged at 7400 g for 5 min at 4°C. RNA pellets were air dried for 15 min and dissolved in RNase free water. RNA solutions then went through on column purification and DNA digestion using RNeasy Mini Kit (74104, QIAGEN INC) and DNase kit (79254, QIAGEN INC).
Total RNA-Seq libraries were generated from 3.8-500 ng of high-quality total RNA, as assessed using the Bioanalyzer (Agilent), according to the manufacturer’s directions using a 200-5-fold dilution of the universal adaptor and 16-9 cycles of PCR per the respective input mass with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L, NEB), the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (E7400L, NEB), and the NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (E6440S, NEB) and purified using the SPRIselect bead-based reagent (B23318, Beckman Coulter). Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and Qubit Fluorometer (Life Technologies).  Equal molar libraries were pooled, quantified, and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit, following the “Adapting Libraries for the G4 – Retaining Original Indices” protocol.  The converted pools were sequenced to the required number of reads per library on F2 flow cells (700102) or F3 flow cells (700126) on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit (700141), using Instrument Control Software 23.08.1-1 with the following read lengths: 8 bp Index1, 100 bp Read1, 8 bp Index2, and 100 bp Read2. Following sequencing, sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.

value: Ovary

tag: genotype

value: WT

value: Starved


title: Ker_CD4+CLA+Th1/17_PAM080

city: Seattle,

first: Stephanie

last: Osmond

institute: Benaroya Research Institute


title: Ker_CD4+CLA+Th22_PAM111


title: Surface_fish_new_starved_2

description:
Library name: L66827
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_new_starved_2


title: Raji_chrRNA-seq_T0_PDS_rep1_1

value: B lymphocyte

tag: cell line

tag: experiment

tag: spike-in cell line


title: Control_NoDrug_Liver_14

description:
Library name: Sample_68
Control_F_Liver_14


title: Control_NoDrug_Liver_13

description:
Library name: Sample_67
Control_F_Liver_13


title: Ker_CD4+CLA+Th17_PAM111

tag: tcellsortforstimulation


title: mur24h1B3 QSP

value: QSP

tag: incubation time


title: Surface_fish_new_starved_1

description:
Library name: L66826
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_new_starved_1


title: Pachon_new_ctrl_2

description:
Library name: L66825
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_new_ctrl_2

value: Non-treated


title: CPB_Lind_Liver_12

description:
Library name: Sample_66
CPB_Lind_Liver_12

value: CPB/DHCA

value: Linrodostat

value: M


title: Mm_thymus_B6_P28_Bmp4_rep2

city: Freiburg

first: Thomas

last: Boehm

address: Stuebeweg 51

data_processing:
Transcriptomes were analyzed on the Galaxy platform.
Adapters were trimmed with TrimGalore! (version 0.4.3.1).
Reads were aligned to the reference genome with Hisat2  (version 2.1.0).
Counts were generated with featureCounts (version 1.6.1.0).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample

source_name: thymus

extract_protocol:
Preparations of single TECs were prepared from explanted thymi. Negative enrichment via MACS sorting with anti-CD45 beads (Miltenyi) was performed. Enriched TECs were purified by FACS and sorted directly into TRI reagent (Sigma-Aldrich). RNA was extracted following standard protocols.
Libraries were constructed with the NEBNext Ultra RNA Library Prep kit or the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.

value: thymus

tag: cell type

value: Epcam+CD45- TECs

tag: age

tag: condition


title: Mm_thymus_B6_P28_Bmp4_rep3

institute: Max Planck Institute for Immunobiology and Epigenetics


title: Ker_CD4+CLA+Th1_PAM111

address: 1201 9th Ave

tag: tcelldonorid

tag: tcellgmcsf

tag: tcellifngamma


title: Pachon_new_starved_2

description:
Library name: L66829
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_new_starved_2

tag: tissue

tag: treatment


title: Mm_thymus_B6_P28_Bmp4_rep1

tag: strain


title: CPB_NoDrug_Liver_11

description:
Library name: Sample_65
CPB_Liver_11

tag: intervention

value: NoDrug

tag: Sex

tag: batch


title: Ker_Control_3

value: Keratinocytes

value: Conditioned Media

tag: tcelltnfalpha


title: Pachon_new_ctrl_1

description:
Library name: L66824
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_new_ctrl_1

tag: genotype


title: Ker_CD4+CLA+Th22_PAM108


title: Raji_chrRNA-seq_T0_PDS_rep1_2

value: Burkitt's lymphoma

tag: cell line

value: Raji

tag: experiment

value: RNA-seq

tag: spike-in cell line

value: ERCC

tag: chip antibody

value: ChrRNA

value: untreated

tag: time point


title: Surface_fish_new_ctrl_2

description:
Library name: L66823
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_new_ctrl_2

value: Ovary

value: WT


title: ATAC-Seq of tobacco callus cells cuture by 0.5 auxin concentrations

city: wuhan

first: yu

last: zhang

address: Gaonong International Phase II, No. 888 Gaoxin Avenue, Donghu High-tech Zone, Wuhan

institute: biorun

description: Tobacco (Nicotiana tabacum L.) Callus

library_source: other

data_processing:
Basecalls were performed using Illunima for Novaseq output.
ATACseq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.39, discarding reads left with <20 bp
ATACSeq reads were aligned to the Nicotiana_benthamiana genome using Niben v2.6.1. Only uniquely mapping reads with at most two mismatches were retained.
To create ATACseq coverage plots, the locations of the mapped ATACSeq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v2.2.7.1 with the significance cut-off q-value <=0.05
Assembly: Niben.v2.6.1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: other

organism: Nicotiana tabacum

source_name: vitro tissue

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris)
Nuclei were isolated and treated with Tn5 transposase, which fragments DNA and inserts sequencing adapters at regions of open chromatin. The transposition reaction was carried out under optimized conditions to ensure efficiency and specificity. Post-transposition, DNA fragments were PCR-amplified using indexed primers, with a limited number of cycles to minimize PCR bias.

value: vitro tissue

value: tobacco explants were harvested from the media containing 0.1 mg/L or 0.5 mg/L NAA after 3 weeks culture


title: Control_NoDrug_Liver_10

description:
Library name: Sample_64
Control_M_Liver_10

value: Liver

value: Control

tag: animal id


title: Surface_fish_new_ctrl_1

description:
Library name: L66822
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_new_ctrl_1

value: Non-treated


title: Ker_CD4+CLA+Th1/17_PAM081

tag: cell type

value: Blood T cell supernatant

tag: tcellsortforstimulation

tag: tcelldonorid


title: ATAC-Seq of tobacco callus cells cuture by 0.1 auxin concentrations

description: Tobacco (Nicotiana tabacum L.) Callus

tag: tissue

value: tobacco explants were harvested from the media containing 0.1 mg/L or 0.5 mg/L NAA after 2 weeks culture


title: CPB_NoDrug_Liver_9

description:
Library name: Sample_63
CPB_Liver_9

value: CPB/DHCA

tag: treatment

value: NoDrug

value: M


title: Ker_CD4+CLA+Th17_PAM108

value: Keratinocytes

tag: tcellgmcsf

tag: tcellifngamma


title: Control_NoDrug_Liver_7

description:
Library name: Sample_62
Control_M_Liver_7

tag: intervention

tag: Sex


title: Pachon_old_starved_4

description:
Library name: L66821
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_old_starved_4

value: Starved


title: Ker_Control_2

value: Conditioned Media

tag: tcelltnfalpha