title: NB099_PD1_8

city: South San Francisco

first: Geoff

last: Stone

address: 333 Oyster Point Blvd

institute: NGM Biopharmaceuticals Inc.

description: anti-PD-1 antibody treatment from sequencing batch NB099, sample 8

data_processing:
For sequencing alignment, RNA-seq data raw reads were filtered using Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove low quality and adaptor bases. Reads shorter than 20nt were discarded
Filtered reads were mapped to UCSC hg19 and mm9 genome sequences using STAR (v2.7.6a)
XenofilteR (v1.6) was used on the bam files to exclude mouse RNA sequence reads that originated from host mice.
Counts of all samples aligned to the human genome were generated using featureCounts (v2.0.1) and edgeR (v3.40.1) was used to get normalized counts and perform differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: Gene expression raw read counts in tabular data format

source_name: Tumor infiltrating human immune cells of engrafted humanized mice

extract_protocol:
Tumors were dissected and dissociated by mincing with a razor blade, followed by grinding through a 70 μm filter cup (Corning) to generate a single cell suspension. Dissociated tumor cells were then washed, counted and human CD45+ cells isolated using the Human CD45 Positive Selection Kit for humanized mice (Stemcell Technologies), according to the manufacturer’s instructions. Following four rounds of washing and magnetic bead isolation, the non-dissociated bead/cell mixture was resuspended in 100 μl of RNAlater (Invitrogen) and stored at -80 °C.  To isolate RNA, wells were thawed, cells were pelleted and pellets lysed in 100 μl of RLT buffer, followed by centrifugation to remove cell debris and magnetic beads. Supernatant was processed to isolate RNA with the RNEasy mini kit following manufacturer's instructions (Qiagen).
Total RNA was prepared for sequencing using the Illumina stranded mRNA library prep kit and sequenced on an Illumina NovaSeq S2 (100bp single-end reads and an average of 40 million reads were generated for each sample).

treatment_protocol: For PBMC models, 7-week old female NOD/SCID Gamma (NSG) mice (Jackson Laboratories) were used. Mice were housed in a 12-hour light/dark cycle facility under pathogen-free conditions in microisolator cages with standard laboratory chow and water ad libitum. Body weight and tumor volume were measured twice weekly. Tumor volume was calculated using the formula [tumor volume (mm3) = π/6 × length × width2] and plotted as geometric mean ± SEM. Mice were first implanted with 5 million cancer cells (A375 or Colo320) by subcutaneous injection in the flank. When median tumor size reached 50-100 mm3, animals were randomized and irradiated at 1 Gy. PBMC were thawed, rested overnight and injected IP at 5 million PBMC per animal. The next day, animals were injected IP at 10 mg/kg total antibody. Injections were continued bi-weekly for a total of 6-8 doses. For CD34 humanized mouse models, female NOG-EXL mice engrafted with CD34+ cord blood cells were purchased from Taconic. 3 independent CD34 donors were used, with 7-8 mice per donor.  Mice were housed and tumors measured as described above. Mice were implanted with 5 million A375 cancer cells by subcutaneous injection in the flank. When median tumor size reached 50-100 mm3, animals were randomized based on CD34 donor and tumor size. Animals were injected IP at 10 mg/kg total antibody. Injections were continued bi-weekly for a total of 6 doses.

tag: treatment


title: CLL019

status: Public on Feb 12 2025

type: SRA

city: Rochester

first: Jessica

last: Hohenstein

state: MN

address: 200 1st St SW

country: USA

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
mRNA sequencing was generated using a HiSeq 4000 sequencer for 58 AA CLL and 292 EA CLL.  The raw RNA sequencing paired-end reads were processed through the Mayo RNA-Seq bioinformatics pipeline, MAP-RSeq version 3.1.4. Batch correction for all RNA samples was performed by removing protein coding genes with low counts, for each batch individually, resulting in 9,934 protein coding genes.  In addition, CombatSeq was run using the annotated reported race as a covariate, with CombatSeq corrected count values used for all downstream analyses.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes batch corrected gene counts each gene per sample

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA was extracted using the Quagen miRNeasy Mini Kit
Illumina TruSeq Stranded mRNA library prep protocol

tag: ancestry

value: European Ancestry (EA)

tag: tissue

value: Peripheral blood mononuclear cells

tag: disease state

value: Chronic Lymphocytic Leukemia (CLL)

tag: genotype

value: IGHV Mutated


title: MS27a_mixed4

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

country: Germany

data_processing:
All raw fastq files were processed with the Nanostring GeoMxNGSPipeline v2.3.3.10, and counts per gene were exported as Nanostring DCC files per sample.
Assembly: hg38
Supplementary files format and content: Nanostring GeoMx DCC files with read counts per gene
Library strategy: Spatial Transcriptomics

source_name: Brain, MS Autopsie

extract_protocol:
5µm thick sections were cut under RNase free codtions and processed according to the GeoMx RNA FFPE workflow (MAN-10150-02) with 10min antigen retrival at 100°C and 15min Proteinase K (0.1µg/ml in PBS) at 37°C for RNA Target exposure.
Spatial Transcriptomics libararys were prepared according to GeoMx DSP workflow (MAN-10153-02)

value: Brain, MS Autopsie

tag: cell type

value: CD68 positive

tag: location

value: mixed rim


title: WT_T_IL-rep3

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (version 2.7.11b), Samtools (version 1.9) and Picard (version 2.9.2). Htseq (version 0.9.1) was applied to calculate raw read counts.
Assembly: mm10
Supplementary files format and content: raw read counts from RNA-seq samples

organism: Mus musculus

source_name: T cells from spleen

growth_protocol: Total RNA-seq was done for the splenocyte and cytokine-stimulated T cells of wild-type and mutant mice carrying a point mutation in Stat5b-Y665.

extract_protocol:
Total RNA was extracted from frozen mammary tissue from mice and purified with RNeasy Plus Mini Kit (Invitrogen, 12183018A). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a HiSeq 3000 or Novaseq 6000 instrument (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.

value: T cells from spleen

tag: strain

tag: Stage

value: 2-month-old age

value: WT


title: NB099_PD1_73

state: CA

description: anti-PD-1 antibody treatment from sequencing batch NB099, sample 73

molecule: polyA RNA

value: Tumor infiltrating human immune cells of engrafted humanized mice


title: WT_T_IL-rep4


title: WT_T_IL-rep2


title: NB099_PD1_72

description: anti-PD-1 antibody treatment from sequencing batch NB099, sample 72


title: CLL017


title: NB099_PD1_53

description: anti-PD-1 antibody treatment from sequencing batch NB099, sample 53


title: MS27a_mixed3


title: CLL018

value: IGHV Unmutated


title: CLL023


title: MS27a_mixed2


title: CLL016


title: NB099_PD1_51

description: anti-PD-1 antibody treatment from sequencing batch NB099, sample 51


title: WT_T_IL-rep1


title: WT_CD4_Stat5b_Y665F-rep3

source_name: CD4 T cells from spleen and lymph node

value: CD4 T cells from spleen and lymph node

value: Stat5a/b flox/flox


title: MS27a_mixed1


title: NB099_PD1_48

description: anti-PD-1 antibody treatment from sequencing batch NB099, sample 48


title: CLL015


title: MS1a_NAWM4

value: NAWM


title: MS1a_NAWM3


title: CLL014


title: WT_CD4_Stat5b_Y665F-rep2


title: MS27a_NAWM5


title: WT_CD4_Stat5b_Y665F-rep1


title: MS1a_NAWM2


title: NB099_PD1_39

description: anti-PD-1 antibody treatment from sequencing batch NB099, sample 39


title: MS1a_NAWM1


title: CLL013


title: WT_CD4_Stat5b_Y665H-rep3


title: NB099_PD1_36

description: anti-PD-1 antibody treatment from sequencing batch NB099, sample 36


title: CLL012


title: WT_CD4_Stat5b_Y665H-rep2


title: CLL011


title: NB099_ILT2_ILT4_PD1_88

description: anti-ILT2/ILT4 antibody and anti-PD-1 treatment from sequencing batch NB099, sample 88

value: anti-ILT2/ILT4, anti-PD-1


title: MS1a_active3

value: active center


title: WT_CD4_Stat5b_N642H-rep3


title: NB099_PD1_11

description: anti-PD-1 antibody treatment from sequencing batch NB099, sample 11


title: NB099_ILT2_ILT4_PD1_71

description: anti-ILT2/ILT4 antibody and anti-PD-1 treatment from sequencing batch NB099, sample 71


title: MS1a_active4


title: WT_CD4_Stat5b_Y665H-rep1


title: CLL010

value: European Ancestry (EA)


title: MS1a_active1


title: MS1a_active2


title: CLL009

value: Peripheral blood mononuclear cells


title: CLL008

value: Chronic Lymphocytic Leukemia (CLL)


title: WT_CD4_Stat5b_N642H-rep1


title: NB099_PD1_44

description: anti-PD-1 antibody treatment from sequencing batch NB099, sample 44


title: WT_CD4_Stat5b_N642H-rep2


title: NB099_ILT2_ILT4_PD1_60

description: anti-ILT2/ILT4 antibody and anti-PD-1 treatment from sequencing batch NB099, sample 60


title: NB099_ILT2_ILT4_PD1_49

description: anti-ILT2/ILT4 antibody and anti-PD-1 treatment from sequencing batch NB099, sample 49


title: CLL007


title: WT_CD4_Stat5b-rep3


title: MS5b_NAWM3


title: MS5b_NAWM4


title: NB099_ILT2_ILT4_PD1_1

description: anti-ILT2/ILT4 antibody and anti-PD-1 treatment from sequencing batch NB099, sample 1


title: WT_CD4_Stat5b-rep2


title: CLL005

value: IGHV Mutated


title: MS5b_NAWM2

value: Brain, MS Autopsie


title: CLL006


title: MS5b_NAWM1

value: CD68 positive


title: NB099_ILT2_ILT4_74

description: anti-ILT2/ILT4 antibody treatment from sequencing batch NB099, sample 74


title: CLL004


title: MS5b_brl8

value: BRL rim


title: NB099_ILT2_ILT4_64

description: anti-ILT2/ILT4 antibody treatment from sequencing batch NB099, sample 64


title: WT_CD4-rep3


title: WT_CD4-rep2


title: CLL003


title: MS5b_brl7


title: NB099_ILT2_ILT4_52

description: anti-ILT2/ILT4 antibody treatment from sequencing batch NB099, sample 52


title: NB099_ILT2_ILT4_59

description: anti-ILT2/ILT4 antibody treatment from sequencing batch NB099, sample 59


title: MS5b_brl6


title: CLL002


title: WT_CD4-rep1


title: MS5b_brl5


title: NB099_ILT2_ILT4_5

description: anti-ILT2/ILT4 antibody treatment from sequencing batch NB099, sample 5


title: CLL001


title: S5KO_CD4_Stat5b_Y665F-rep2


title: HMC-3 IP

city: Chengdu

first: Ling

last: Wei

country: China

institute: Sichuan provincial peaple's hospital

data_processing:
*library strategy: meRIP-seq
Clean reads of input libraries were aligned to reference genome (UCSC HG19) by STAR software. Then circRNAs were identified by DCC software using the STAR alignment results.
Clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software.
Differentially methylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and chosen by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes, the associated genes of differentially methylated LncRNAs and the source genes of differentially methylated circRNAs separately.
Assembly: UCSC HG19
Supplementary files format and content: tab-delimited text files include differentially methylated sites of mRNA in ARC group versus HMC group (up and down).

source_name: lens capsule

extract_protocol:
Human lens epithelia were collected during standard cataract surgery, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
The m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Novaseq instrument with 150bp paired-end reads.

value: lens capsule

tag: subject status

value: highly myopic cataract (HMC) patient

value: IP


title: NB099_ILT2_ILT4_45

description: anti-ILT2/ILT4 antibody treatment from sequencing batch NB099, sample 45

value: Tumor infiltrating human immune cells of engrafted humanized mice


title: MS5a_brl4


title: HMC-2 IP


title: S5KO_CD4_Stat5b_Y665F-rep3

value: 2-month-old age


title: S5KO_CD4_Stat5b_Y665F-rep1

value: CD4 T cells from spleen and lymph node


title: WT_CD4_Stat5b-rep1

value: Stat5a/b flox/flox


title: NB099_ILT2_ILT4_75

description: anti-ILT2/ILT4 antibody treatment from sequencing batch NB099, sample 75


title: MS5a_brl3


title: HMC-1 IP


title: S5KO_CD4_Stat5b_Y665H-rep3


title: MS5a_brl2


title: NB099_ILT2_ILT4_23

description: anti-ILT2/ILT4 antibody treatment from sequencing batch NB099, sample 23


title: MS5a_brl1


title: NB099_ILT2_ILT4_42

description: anti-ILT2/ILT4 antibody treatment from sequencing batch NB099, sample 42


title: S5KO_CD4_Stat5b_Y665H-rep2


title: ARC-3 IP

value: age-related cataract (ARC) patient


title: NB099_Isotype_99

description: control isotype antibody treatment from sequencing batch NB099, sample 99

value: Isotype


title: ARC-2 IP


title: NB099_Isotype_77

description: control isotype antibody treatment from sequencing batch NB099, sample 77


title: MS5a_NAWM3

value: NAWM


title: NB099_Isotype_62

description: control isotype antibody treatment from sequencing batch NB099, sample 62


title: S5KO_CD4_Stat5b_N642H-rep2


title: NB099_Isotype_58

description: control isotype antibody treatment from sequencing batch NB099, sample 58


title: S5KO_CD4_Stat5b_N642H-rep3


title: MS5a_NAWM2


title: PTU Rep 10

city: Research Triangle Park

first: Katherine

middle: Lynn

last: O'Shaughnessy

state: NC

address: 109 TW Alexander Drive

institute: United States Environmental Protection Agency

description:
60 PTU
PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

data_processing:
All downstream bioinformatics were performed in Partek Flow Genomic Analysis Software.
The median number of reads per sample was 78.1 million and the average 78.4 million; the Phred scores were all >35.
Samples were aligned to the Rattus norvegicus reference genome (mRatBN7.2/rn7) using STAR 2.7.8a. Counts were quantified using the Partek Expectation/Maximization (E/M) model and the rat RefSeq annotation (GCF_015227675.2) and normalized using median ratio.
Principal component analysis was performed on normalized reads of the entirety of the RNA-Seq data to visualize variation. Differential gene expression was identified by comparing either PTU to control, or PFHxS to controls, using DESeq2.
Multiple testing was corrected using the Benjamini–Hochberg step-up procedure to control the False Discovery Rate (FDR). DEGs were identified by an FDR (q-value) <0.05.
Assembly: mRatBN7.2/rn7
Supplementary files format and content: tab-delimited text file includes DESeq2 counts
Supplementary files format and content: tab-delimited text file with statistical support

organism: Rattus norvegicus

source_name: Long Evans

extract_protocol:
RNA was isolated using Qiagen’s RNeasy Plus Universal (Qiagen, ID 73404) according to manufacturer’s instructions. All RNA samples were quantified using a NanoDrop (Thermo Fisher Scientific), and quality assessed using an Agilent 2100 Bioanalyzer. All RNA samples had an RNA Integrity Number (RIN) ≥9.
The library preparation was completed using the QIAseq Stranded mRNA Select Kit (Qiagen) utilizing 500 ng of RNA as input. Library quality controlled was performed using an Agilent 2100 Bioanalyzer. Libraries were pooled in equimolar concentrations, and pools quantified by qRT-PCR before sequencing on an Illumina NovaSeq according to the manufacturer instructions.

treatment_protocol: Pregnant rats were exposed to vehicle (control, molecular grade water), PFHxS (50 mg/kg/day), or PTU (0.875 mg/kg/day) throughout pregnancy and lactation. Brain tissue from 1 female pup per litter was examined by RNA-Seq to determine if thyroid action was interrupted.

value: Long Evans

tag: Sex

value: Female

tag: cell population

value: Brain, ventricular/subventricular zone

tag: developmental stage

value: postnatal day 6 (PN6)

value: maternal PTU exposure (PTU)

tag: physiological stage

value: Hypothyroid


title: S5KO_CD4_Stat5b_N642H-rep1


title: ARC-1 IP


title: MS5a_NAWM1

value: Brain, MS Autopsie

value: CD68 positive


title: KC001, scRNAseq

city: Trieste

first: UDAY

last: RANGASWAMY

state: Trieste

address: via bonomea 265

department: NEUROSCIENCE

country: Italy

institute: SISSA

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The read alignment and gene counting were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCz11 (version 105)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Pharyngeal arches

extract_protocol:
From the offspring of an intercross of nkx2.7+/-;Tg(tcf21:NTRO-mCherry)pd108, two wild-type and two nkx2.7-/- embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected, dissociated, and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum (FBS) (5% of volume) was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally, DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter (BD Biosciences) under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 (Thermo Fisher, DIL5522) solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads (BD Biosciences, 655051), SPHERO Rainbow Calibration Particles (8 Peaks) 3.0 m, 5 mL (Spherotech, RCP-30-5A), followed by optimization of the drop charge delay using BD FACS Accudrop Beads (BD Biosciences, 345249).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: wild-type

value: Pharyngeal arches

value: AB

value: 26 hpf


title: KC002, scRNAseq

description: 10x Genomics


title: S5KO_CD4_Stat5b-rep3

value: CD4 T cells from spleen and lymph node

value: 2-month-old age


title: MS5a_active4

value: active center


title: PTU Rep 9

description:
59 PTU
PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: NB099_Isotype_4

description: control isotype antibody treatment from sequencing batch NB099, sample 4

value: Tumor infiltrating human immune cells of engrafted humanized mice

value: Isotype


title: S5KO_CD4_Stat5b-rep2

value: Stat5a/b flox/flox


title: MS5a_NAWM4

value: NAWM


title: S5KO_CD4_Stat5b-rep1


title: MS5a_active3


title: NB099_Isotype_38

description: control isotype antibody treatment from sequencing batch NB099, sample 38


title: PTU Rep 6

description:
56 PTU
PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: Long Evans

value: Female

value: Brain, ventricular/subventricular zone


title: MS5a_active2


title: S5KO_CD4_Stat5b_Y665H-rep1


title: S5KO_CD4-rep2


title: NB099_Isotype_29

description: control isotype antibody treatment from sequencing batch NB099, sample 29


title: PTU Rep 7

description:
57 PTU
PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: postnatal day 6 (PN6)

value: maternal PTU exposure (PTU)

value: Hypothyroid


title: MS2b_NAWM8

value: Brain, MS Autopsie

value: CD68 positive


title: PTU Rep 4

description:
53 PTU
PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: S5KO_CD4-rep3


title: PTU Rep 8

description:
58 PTU
PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: MS5a_active1


title: Y665F_T_IL-PolII-rep1

library_source: genomic

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and Bowtie (version 1.2.2) and Samtools (version 1.8), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome mm10. Homer (version 4.9.1) software was applied to generate bedGraph files, seperately. Integrative Genomics Viewer (version 2.3.98) was used for visualization with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools to remove duplicates. Homer software was applied  for the generation of bedGraph files.
Assembly: mm10
Supplementary files format and content: bedgraph of ChIP-seq

molecule: genomic DNA

growth_protocol: T cells from spleen of wild-type and mutant mice at carrying a point mutation in Stat5b-Y665.

extract_protocol:
Chromatin was fixed with formaldehyde (1% final concentration) for 10min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: STAT5B (ThermoFisher scientific, 13-5300), H3K27ac (Abcam, ab4729) and RNA polymerase II (Abcam, ab5408). Libraries for next-generation sequencing were prepared and sequenced with a Novaseq 6000 instrument (Illumina). Libraries for sequencing were prepared using standard Illumina protocols.
Libraries for sequencing were prepared using standard New England Biolabs' protocols.

value: T cells from spleen

tag: chip-seq antibody

value: RNA polymerase II (Abcam, ab5408)


title: NB099_Isotype_24

description: control isotype antibody treatment from sequencing batch NB099, sample 24


title: Y665F_T_IL-PolII-rep2


title: NB099_Isotype_19

description: control isotype antibody treatment from sequencing batch NB099, sample 19


title: PTU Rep 5

description:
55 PTU
PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: MS2b_NAWM9


title: NB099_48A5_56

description: anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB099, sample 56


title: S5KO_CD4-rep1

value: CD4 T cells from spleen and lymph node


title: NB099_48A5_57

description: anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB099, sample 57


title: MS2b_NAWM7


title: Y665F_T_IL-H3K27ac-rep2

value: 2-month-old age

value: H3K27ac (Abcam, ab4729)


title: PTU Rep 1

description:
50 PTU
PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: MS2b_NAWM5


title: MS2b_NAWM6


title: MS2b_active4

value: active center


title: PTU Rep 3

description:
52 PTU
PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: NB099_Isotype_41

description: control isotype antibody treatment from sequencing batch NB099, sample 41

value: Tumor infiltrating human immune cells of engrafted humanized mice

value: Isotype


title: NB099_48A5_20

description: anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB099, sample 20


title: NB099_48A5_95

description: anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB099, sample 95


title: MS2b_active3


title: PTU Rep 2

description:
51 PTU
PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: PFHxS Rep 9

description:
37 PFHxS
PFHxS vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: maternal PFHxS exposure (PFHxS)

value: Hypothyroxinemic


title: Y665F_T_IL-STAT5B-rep3

value: STAT5B (ThermoFisher scientific, 13-5300)


title: Y665F_T_IL-STAT5B-rep2


title: NB099_48A5_16

description: anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB099, sample 16


title: PFHxS Rep 10

description:
45 PFHxS
PFHxS vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: Long Evans

value: Female

value: Brain, ventricular/subventricular zone


title: Y665F_T_IL-STAT5B-rep1


title: Y665H_T_IL-PolII-rep1


title: NB099_48A5_17

description: anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB099, sample 17


title: PFHxS Rep 6

description:
25 PFHxS
PFHxS vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: postnatal day 6 (PN6)


title: PFHxS Rep 8

description:
33 PFHxS
PFHxS vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: NB099_27F9_48A5_6

description: anti-ILT2 clone 27F9 and anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB099, sample 6


title: Y665F_T_IL-H3K27ac-rep1


title: Y665H_T_IL-H3K27ac-rep1


title: PFHxS Rep 5

description:
21 PFHxS
PFHxS vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: NB099_27F9_48A5_87

description: anti-ILT2 clone 27F9 and anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB099, sample 87


title: MS2b_active1

value: Brain, MS Autopsie


title: NB099_48A5_27

description: anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB099, sample 27


title: MS2b_active2

value: CD68 positive


title: MS19_NAWM2

value: NAWM


title: PFHxS Rep 7

description:
29 PFHxS
PFHxS vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: MS19_NAWM4


title: NB099_27F9_48A5_12

description: anti-ILT2 clone 27F9 and anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB099, sample 12


title: WT_T_IL-H3K27ac-rep1

value: T cells from spleen

value: WT


title: MS19_NAWM3


title: MS19_mixed4

value: mixed rim


title: NB099_27F9_48A5_2

description: anti-ILT2 clone 27F9 and anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB099, sample 2


title: PFHxS Rep 4

description:
17 PFHxS
PFHxS vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: MS19_NAWM1


title: WT_T_IL-PolII-rep1

value: 2-month-old age

value: RNA polymerase II (Abcam, ab5408)


title: WT_T_IL-STAT5B-rep1


title: PFHxS Rep 2

description:
9 PFHxS
PFHxS vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: NB099_27F9_98

description: anti-ILT2 clone 27F9 antibody treatment from sequencing batch NB099, sample 98

value: Tumor infiltrating human immune cells of engrafted humanized mice


title: Control Rep 9

description:
48 Control
PFHxS vs. Control Worksheet, PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: vehicle control (Control)

value: Hypothyroid


title: NB099_27F9_80

description: anti-ILT2 clone 27F9 antibody treatment from sequencing batch NB099, sample 80


title: MS19_mixed3


title: PFHxS Rep 1

description:
5 PFHxS
PFHxS vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: maternal PFHxS exposure (PFHxS)

value: Hypothyroxinemic


title: Control Rep 8

description:
36 Control
PFHxS vs. Control Worksheet, PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: Long Evans

value: Euthyroid


title: MS19_mixed2


title: dsfb_3

city: Hangzhou

first: Lin-Yu

last: Lu

state: Zhejiang

address: 268 Kaixuan Road, North Central Building, Room 536

institute: Zhejiang University

data_processing:
Raw data (in FASTQ format) were generated from the Illumina platform. Sequence artifacts, including low-quality reads, unrecognizable nucleotides (N) and adapter contamination were excluded for downstream analysis.
The filtered (clean) reads were mapped to mm10 reference genome using STAR (version 2.6.0)  with default parameters. Read counts were extracted after the mapping process.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes read counts for each sample

source_name: testes

extract_protocol:
Testes of PD19 control and dsfb mice were harvested and kept in liquid nitrogen before processing. TRIzol reagent was added to homogenize the tissue and total RNA was extracted.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s protocols.

value: testes

value: dsfb

tag: time


title: NB099_27F9_91

description: anti-ILT2 clone 27F9 antibody treatment from sequencing batch NB099, sample 91


title: Y665H_T_IL-STAT5B-rep1

value: STAT5B (ThermoFisher scientific, 13-5300)


title: NB099_27F9_61

description: anti-ILT2 clone 27F9 antibody treatment from sequencing batch NB099, sample 61


title: MS19_mixed1

value: Brain, MS Autopsie

value: CD68 positive


title: PFHxS Rep 3

description:
13 PFHxS
PFHxS vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: Female

value: Brain, ventricular/subventricular zone

value: postnatal day 6 (PN6)


title: NB099_27F9_48A5_13

description: anti-ILT2 clone 27F9 and anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB099, sample 13


title: dsfb_2


title: NB099_27F9_50

description: anti-ILT2 clone 27F9 antibody treatment from sequencing batch NB099, sample 50


title: Nchr3

city: Toronto

first: Kirti

last: Mittal

state: Ontario

address: Santos Lab, 25 Orde Street, Room 6-1001 MRS

country: Canada

institute: Lunenfeld-Tanenbaum Research Instit

data_processing:
Adaptor sequences and low-quality score bases (Phred score < 33) were trimmed using Trimmomatic v.0.39.
The resulting reads were aligned to the T2T genome assembly using STAR v.2.7.8a with Ensembl annotation (v104).
Raw counts of repetitive elements were obtained using the FeatureCounts function from the Subread package (v2.14.2).
Assembly: T2T
Supplementary files format and content: txt

molecule: nuclear RNA

growth_protocol: H9 hES cells were cultured in RSeT media (STEM CELL) following manual instruction for mainting RSeT naive condition

extract_protocol:
Cell were subfractionated using chromatin extraction protocol, and  RNA extracted using the RNeasy kit (QIAGEN, cat#74106), following the manufacturer instruction. RNA integrity was assessed with the Agilent 2100 Bioanalyzer System (Agilent Technologies).
RNA library preparations were carried out using theNEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® # E7760, according to manufacturer's protocol. The libraries were size-selected using Ampure XP Beads (Beckman Coulter, cat# A63880) and quantified using the KAPA Library Quantification kit - Universal (KAPA Biosystems, cat# KK4828).

tag: cell line

value: Human Embryonic stem cells

value: naïve


title: Control Rep 7

description:
32 Control
PFHxS vs. Control Worksheet, PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

tag: treatment


title: dsfb_1


title: control_2

value: control


title: NB099_27F9_46

description: anti-ILT2 clone 27F9 antibody treatment from sequencing batch NB099, sample 46

value: Tumor infiltrating human immune cells of engrafted humanized mice


title: Nchr2


title: nc7w, pulp cell, scRNAseq

city: ChangChun

first: Zhengwen

last: An

state: JiLin

address: HeGuang Road 763

department: Department of Oral Biology

institute: Jilin University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger (7.0.1). (https://www.10xgenomics.com)
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Incisor Pulp

extract_protocol:
Mouse mandibles were carefully dissected from 15 C57BL/6 mice aged 7 weeks using precise dissection under a stereomicroscope. The surrounding bones and soft tissues were carefully removed with scalpels and fine-point tweezers. The incisor pulp, with minimal inclusion of dental epithelium, was isolated, fragmented, and immersed in cold PBS. Subsequently, these fragments were digested in α-MEM (Gibco) containing collagenase at 37°C for 30-45 mins
The single cell suspension was quantified and loaded into the 10X Chromium system, targeting approximately 10,000 cells for barcoding in preparation for scRNA-seq using a Single Cell 5′ Library Kit (10X Genomics). Cells were successfully barcoded and their transcriptomes were sequenced using the  Illumina Novaseq System (Illumina, San Diego, CA).

value: Incisor Pulp

value: Dental pulp cell

value: WT


title: Pchr3

value: primed


title: Control Rep 6

description:
24 Control
PFHxS vs. Control Worksheet, PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: Long Evans

value: vehicle control (Control)

value: Euthyroid


title: control_3

value: testes


title: Control Rep 3

description:
12 Control
PFHxS vs. Control Worksheet, PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx


title: alphaTC, NKX2.2 ChIP, 1

city: Aurora

first: Lori

last: Sussel

state: Colorado

address: 1775 Aurora ct.

institute: CU Anschutz

data_processing:
Fastqc for quality control
bbduk for adapter trimming
Bowtie2 for alignment
MACS2 for peakcalling
Assembly: mm10
Supplementary files format and content: .bed file containing binding peaks of NKX2.2 in alpha cells

extract_protocol:
magnetic bead enrichment and DNA column clean-up
Tecan Ovation Ultralow System V2

value: alpha cells


title: Pchr1


title: alphaTC, Input, 2


title: MS17_NAWM_rep2

data_processing:
*library strategy: Spatial Transcriptomics
All raw fastq files were processed with the Nanostring GeoMxNGSPipeline v2.3.3.10, and counts per gene were exported as Nanostring DCC files per sample.
Assembly: hg38
Supplementary files format and content: Nanostring GeoMx DCC files with read counts per gene

value: Brain, MS Autopsie

value: CD68 positive

value: NAWM/PPWM


title: MS17_NAWM_rep1


title: Nchr1


title: NB098_hz48A5_4

description: anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB094, sample 4


title: Control Rep 5

description:
20 Control
PFHxS vs. Control Worksheet, PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: Female

value: Brain, ventricular/subventricular zone

value: postnatal day 6 (PN6)


title: microRNA in SKP-SC-EVs

city: nantong

first: songlin

last: zhou

state: jiangsu

address: 19 qixiu road

institute: Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education

description: The extracellular vesicles from skin precursor-derived Schwann cells

data_processing:
The basic reads were converted into sequence data (also called raw data/reads) by base calling.
The length distribution of the clean sequences in the reference genome was determined.
The mature miRNAs were identified by aligning against miRBase v22 database (http://www.mirbase.org/) , and the expression patterns in different samples were analyzed.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include tpm values for sample
Supplementary files format and content: tab-delimited text files include counts values for sample

source_name: skin

extract_protocol:
Total RNA was extracted using mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol.
The libraries were finally sequenced using the Illumina Novaseq 6000 platform.

value: skin

value: skin precursor-derived Schwann cells

value: extracellular vesicles

value: case


title: alphaTC, Input, 1

value: WT


title: NB099_27F9_37

description: anti-ILT2 clone 27F9 antibody treatment from sequencing batch NB099, sample 37

value: Tumor infiltrating human immune cells of engrafted humanized mice


title: Control Rep 4

description:
16 Control
PFHxS vs. Control Worksheet, PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: Long Evans


title: Kidney, Tacrolimus, 28 days, rep 6 [TAC_6_1]

city: Berlin

first: Hasan

last: Demirci

address: Philippstr. 12

department: Institute for Functional Anatomy

institute: Charité - Universitätsmedizin Berlin

description: Processed_Data_File_Tacrolimus_group.txt

data_processing:
Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. We use HISAT2 to
accomplish the mapping.In order to avoid losing a lot of effective junction reads, we use HISAT2 software to alignment for RNA-seq sequencing data analysis and the junction reads can be positioned precisely.
Assembly: rn6
Supplementary files format and content: FPKM values for each Sample

source_name: kidney

extract_protocol:
Total RNAs were isolated from the entire kidneys of adult (10 to12 weeks) male Wistar rats using PeqGOLD TriFast (VWR Life SCIENCE) according to the manufacturer’s instructions.The purity of RNA was checked using NanoPhotometer R spectrophotometer (IMPLEN, Westlake Village, CA, USA Additionally, using the Bioanalyzer 2100 system, the RNA Nano 6000 Assay Kit was used to evaluate the quantity and integrity of RNA (Agilent Technologies, Santa Clara, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using the NEBNext RNA Library Prep Kit for Illumina following the manufacturer’s recommendations (New England BioLabs, Ipswich, MA), and index codes were added to attribute sequences to each sample. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s protocols.

value: kidney

tag: strain background

value: Wistar

value: Tacrolimus


title: control_1

tag: tissue

value: testes

value: control


title: NB098_Isotype_5

description: control isotype antibody treatment from sequencing batch NB098, sample 5

value: Isotype


title: NB099_27F9_10

description: anti-ILT2 clone 27F9 antibody treatment from sequencing batch NB099, sample 10


title: Pchr2

value: Human Embryonic stem cells

value: primed


title: MS17_RIM_rep1

value: Brain, MS Autopsie

value: CD68 positive

value: lesion rim


title: Kidney, Tacrolimus, 28 days, rep 4 [TAC_4_1]


title: alphaTC, NKX2.2 ChIP, 2

value: alpha cells


title: MS20_RIM_rep3


title: NB099_27F9_54

description: anti-ILT2 clone 27F9 antibody treatment from sequencing batch NB099, sample 54


title: Control Rep 2

description:
8 Control
PFHxS vs. Control Worksheet, PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: Female

value: Brain, ventricular/subventricular zone

value: postnatal day 6 (PN6)

value: vehicle control (Control)

value: Euthyroid


title: NB098_Isotype_2

description: control isotype antibody treatment from sequencing batch NB098, sample 2

value: Tumor infiltrating human immune cells of engrafted humanized mice


title: Control Rep 1

description:
4 Control
PFHxS vs. Control Worksheet, PTU vs. Control Worksheet
Oshaughnessy Processed Data Files.xlsx

value: Long Evans


title: NB098_hz48A5_5

description: anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB094, sample 5


title: Kidney, Tacrolimus, 28 days, rep 1 [TAC_1_1]

value: kidney

value: Wistar

value: WT

value: Tacrolimus


title: MS20_NAWM_rep4

value: NAWM/PPWM


title: MS17_RIM_rep2


title: Kidney, Vehicle (DMSO + PEG), 28 days, rep 5 [Veh_5_1]

value: Vehicle (DMSO + PEG)


title: NB098_hz48A5_3

description: anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB094, sample 3


title: Kidney, Tacrolimus, 28 days, rep 5 [TAC_5_1]


title: Min6, Klf4-overexpression, RNA-seq, 4

data_processing:
Fastqc for quality control
bbduk for adapter trimming
STAR for alignment
featurecounts for counts table
EdgeR for DE analysis
Assembly: mm10
Supplementary files format and content: raw counts table in .txt format

extract_protocol:
Total RNA from isolated islets was extracted using a Qiagen Rneasy Mini Kit
Tecan Universal Plus mRNA-seq library preparation kit with NuQuant

treatment_protocol: Lipofectamine 3000 was used in this 48 hour transfection

tag: batch

value: beta cells

value: pGloMyc-Klf4 transfection


title: Min6, Klf4-overexpression, RNA-seq, 3

tag: genotype


title: NB098_hz48A5_6

description: anti-ILT4 clone 48A5 antibody treatment from sequencing batch NB094, sample 6


title: MS20_RIM_rep4

value: Brain, MS Autopsie

tag: cell type

value: CD68 positive

value: lesion rim


title: NB098_Isotype_3

description: control isotype antibody treatment from sequencing batch NB098, sample 3

value: Isotype


title: Min6, Klf4-overexpression, RNA-seq, 2


title: MS20_RIM_rep1

tag: location


title: Kidney, Tacrolimus, 28 days, rep 3 [TAC_3_1]


title: Min6, Klf4-overexpression, RNA-seq, 1


title: MS20_RIM_rep2


title: alphaTC, Klf4-KD, 4

data_processing:
Fastqc for quality control
bbduk for adapter trimming
STAR for alignment
featurecounts for counts table
DESeq2 for DE analysis
Assembly: mm10
Supplementary files format and content: raw counts table in .txt format

treatment_protocol: RNAiMax Lipofectamine was used in this 48 hour reverse transfection

value: alpha cells

value: Klf4 siRNA transfection


title: NB098_Isotype_1

description: control isotype antibody treatment from sequencing batch NB098, sample 1

data_processing:
For sequencing alignment, RNA-seq data raw reads were filtered using Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove low quality and adaptor bases. Reads shorter than 20nt were discarded
Filtered reads were mapped to UCSC hg19 and mm9 genome sequences using STAR (v2.7.6a)
XenofilteR (v1.6) was used on the bam files to exclude mouse RNA sequence reads that originated from host mice.
Counts of all samples aligned to the human genome were generated using featureCounts (v2.0.1) and edgeR (v3.40.1) was used to get normalized counts and perform differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: Gene expression raw read counts in tabular data format


title: Kidney, Tacrolimus, 28 days, rep 2 [TAC_2_1]


title: NB094_hz27F9_6

description: anti-ILT2 clone 27F9 antibody treatment from sequencing batch NB094, sample 6


title: NB094_hz27F9_3

description: anti-ILT2 clone 27F9 antibody treatment from sequencing batch NB094, sample 3


title: Kidney, Vehicle (DMSO + PEG), 28 days, rep 6 [Veh_6_1]


title: Min6, empty vector control, RNAseq, 4

value: pcDNA 3 Empty Vector  transfection


title: Min6, empty vector control, RNAseq, 2


title: NB094_ILT2_ILT4_3

description: anti-ILT2/ILT4 antibody treatment from sequencing batch NB094, sample 3

value: Tumor infiltrating human immune cells of engrafted humanized mice


title: Kidney, Vehicle (DMSO + PEG), 28 days, rep 3 [Veh_3_1]


title: alphaTC, Klf4-KD, 3


title: MS20_NAWM_rep3


title: NB094_hz27F9_1

description: anti-ILT2 clone 27F9 antibody treatment from sequencing batch NB094, sample 1


title: Kidney, Vehicle (DMSO + PEG), 28 days, rep 2 [Veh_2_1]


title: MS20_NAWM_rep2


title: Min6, empty vector control, RNAseq, 3


title: NB094_ILT2_ILT4_6

description: anti-ILT2/ILT4 antibody treatment from sequencing batch NB094, sample 6


title: NB094_Isotype_5

description: control isotype antibody treatment from sequencing batch NB094, sample 5


title: Min6, empty vector control, RNAseq, 1


title: Kidney, Vehicle (DMSO + PEG), 28 days, rep 1 [Veh_1_1]

description: Processed_Data_File_Tacrolimus_group.txt


title: Kidney, Vehicle (DMSO + PEG), 28 days, rep 4 [Veh_4_1]


title: MS20_NAWM_rep1


title: alphaTC, Klf4-KD, 2


title: MS16b_RIM_rep2


title: alphaTC, Klf4-KD, 1


title: MS16b_RIM_rep4


title: MS16b_RIM_rep1


title: MS16b_RIM_rep3


title: alphaTC, scramble control, 4

value: siScramble transfection


title: Kidney, Cyclosporine A, 28 days, rep 3 [CSA_3_1]

description: Processed_Data_File_CyclosporineA_group.txt

value: kidney

value: Cyclosporine A


title: NB094_Isotype_3

description: control isotype antibody treatment from sequencing batch NB094, sample 3


title: Kidney, Cyclosporine A, 28 days, rep 4 [CSA_4_1]

value: Wistar

value: WT


title: NB094_ILT2_ILT4_2

description: anti-ILT2/ILT4 antibody treatment from sequencing batch NB094, sample 2


title: Kidney, Cyclosporine A, 28 days, rep 2 [CSA_2_1]


title: NB094_Isotype_2

description: control isotype antibody treatment from sequencing batch NB094, sample 2


title: MS16b_NAWM_rep3

value: NAWM/PPWM


title: MS16b_NAWM_rep4


title: H2081_GRN overexpression_rep3

city: New York

first: Seungyeul

last: Yoo

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequence reads are mapped and aligned to human genome assembly hg19 and then readcounts for each gene are estimated by Htseq-count
Assembly: hg19
Supplementary files format and content: tab-delimited text file including read count of each gene for each Sample

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit. Poly-adenylated RNA was enriched from 1ug of RNA with the NEBNext PolyA mRNA Magnetic Isolation Module, incubated at 94°C for 15 min and double-strand cDNA was synthesized using SuperScript III reverse transcriptase (ThermoFisher) and NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module.
Up to 10 ng of cDNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and subjected to sequencing.

value: Lung


title: alphaTC, scramble control, 3


title: Kidney, Cyclosporine A, 28 days, rep 1 [CSA_1_1]


title: NB094_Isotype_1

description: control isotype antibody treatment from sequencing batch NB094 , sample 1


title: alphaTC, scramble control, 2


title: Kidney, Vehicle (saline), 28 days, rep 3 [VEH_3_1]

value: Vehicle (saline)


title: H2081_GRN overexpression_rep2


title: MS2_RIM_rep4


title: Kidney, Vehicle (saline), 28 days, rep 1 [VEH_1_1]


title: Min6, Klf4 overexpression, 1

data_processing:
combined fastq files from first and second run (re-ran samples to increase sequencing depth)
Fastqc for quality control
bbduk for adapter trimming
Bowtie2 for alignment
MACS2 for peakcalling
Diffbind for differential accessibility analysis
Assembly: mm10
Supplementary files format and content: .broadPeak files containing the chromatin accessibility region peaks used in differential accessibility analysis

extract_protocol:
ATAC was perfromed using Active Motifs ATAC-seq kit
Tecan Universal Plus mRNA-seq library preparation kit with NuQuant

value: beta cells

value: pGloMyc-Klf4 transfection


title: Min6, Empty Vector, 4


title: MS2_NAWM_rep2

value: Brain, MS Autopsie

value: CD68 positive


title: Min6, Klf4 overexpression, 4


title: alphaTC, scramble control, 1


title: Min6, Empty Vector, 2


title: MS16b_NAWM_rep1


title: Kidney, Vehicle (saline), 28 days, rep 4 [VEH_4_1]


title: HMC-2 Input

value: lens capsule

value: highly myopic cataract (HMC) patient

value: input


title: Min6, Empty Vector, 1

value: pcDNA 3 Empty Vector  transfection


title: MS2_NAWM_rep1


title: A063

type: genomic

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description: Copy number profiling of patient A063, FFPE tumor tissue

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G (Affymetrix).

data_processing: Array fluorescence intensity (CEL) files were automatically generated from DAT files by the Affimetrix GeneChip™ Command Console (AGCC) Software version 4.0. Quality metrics and CNA calls were generated using the Chromosome Analysis Suite (ChAS) software (Thermofisher) using default settings.

label: Biotin

source_name: FFPE tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Depending on expected tumor fraction, 2 or 3 5µm representative FFPE sections were used for DNA extraction. Tumor area was micro-dissected, when possible, whereas in case of small biopsies all sections were subjected to DNA extraction. DNA was obtained through digestion with Proteinase-K 200 µg/ml overnight at 56°C followed by a Proteinase-K blocks for 10 minutes at 95°C. DNA quality/quantity was checked by means of 4200 TapeStation System, NanoDrop ND-1000 v 3.3.1 and Qubit High Sensitivity dsDNA kit.

tag: histotype

value: Brest adenocarcinoma


title: H2081_Control_rep1


title: H2081_GRN overexpression_rep1


title: ARC-3 Input

data_processing:
*library strategy: meRIP-seq
Clean reads of input libraries were aligned to reference genome (UCSC HG19) by STAR software. Then circRNAs were identified by DCC software using the STAR alignment results.
Clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software.
Differentially methylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and chosen by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes, the associated genes of differentially methylated LncRNAs and the source genes of differentially methylated circRNAs separately.
Assembly: UCSC HG19
Supplementary files format and content: tab-delimited text files include differentially methylated sites of mRNA in ARC group versus HMC group (up and down).

value: age-related cataract (ARC) patient


title: Min6, Klf4 overexpression, 3


title: H2081_Control_rep3


title: Kidney, Vehicle (saline), 28 days, rep 2 [VEH_2_1]

value: kidney


title: Min6, Klf4 overexpression, 2


title: MS2_RIM_rep3

value: lesion rim


title: FLT3 ITD Ptprc KO4

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

description: FLT3 ITD Ptprc KO4

data_processing:
fastq conversion of BCL files (bcl2fastq v2.20.0.422)
adapter removal and low quality base trimming (cutadapt 4.2)
read aligned (STAR 2.7.6a) to the mouse reference genome
deduplication of aligned reads (UMI-tools v1.1.1)
gene quantification (featurecounts v2.0.3; Ensembl 100)
Assembly: GRCm38.p6
Supplementary files format and content: tab-separated file with read counts after deduplication (row: genes, column: samples)
Supplementary files format and content: tab-separate file with TPM normalized read counts (row: genes, column: samples)

source_name: osteoclasts from CD11b+ BM

growth_protocol: CD11b-positve BM cells were seeded with a cell density of 3 x 105 cells/cm2 and cultured in alpha-MEM (Sigma Aldrich, Germany) with 10 % heat-inactivated FCS (Sigma Aldrich, Germany), 1 % penicillin/streptomycin (Sigma Aldrich, Germany), and 50 ng/ml murine M-CSF (Immunotools, Germany) for 3 days. OC were then generated using the media described before with addition of 20 ng/ml murine RANKL (R&D systems, Germany) for the remainder of the culture (3 - 10 days). Medium was changed on day 3 and day 5. Where indicated, medium was supplemented with 20 µM AC220 in FLT3 ITD inhibition experiments.

extract_protocol:
Total RNA of OC was obtained when first mature OC appeared in the culture (day 3- 5)
Input of 500 ng total RNA was used for library preparation with NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®, and NEBNext® Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors).

value: osteoclasts from CD11b+ BM

value: FLT3 ITD Ptprc KO


title: H2081_Control_rep2


title: ARC-2 Input


title: FLT3 ITD Ptprc KO3

description: FLT3 ITD Ptprc KO3


title: MS3a_NAWM_rep2

extract_protocol:
5µm thick sections were cut under RNase free codtions and processed according to the GeoMx RNA FFPE workflow (MAN-10150-02) with 10min antigen retrival at 100°C and 15min Proteinase K (0.1µg/ml in PBS) at 37°C for RNA Target exposure.
Spatial Transcriptomics libararys were prepared according to GeoMx DSP workflow (MAN-10153-02)

value: NAWM/PPWM


title: A066

description: Copy number profiling of patient A066, FFPE tumor tissue

value: Colon Adenocarcinoma


title: A060

description: Copy number profiling of patient A060, FFPE tumor tissue

value: Lung adenocarcinoma


title: A064

description: Copy number profiling of patient A064, FFPE tumor tissue

value: Gastric carcinoma


title: MS2_RIM_rep2


title: MS16b_NAWM_rep2


title: A065

description: Copy number profiling of patient A065, FFPE tumor tissue


title: Min6, Empty Vector, 3

value: beta cells

value: WT


title: MS2_RIM_rep1

value: Brain, MS Autopsie

value: CD68 positive


title: Proliferating CD4 T cells (120hr)

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Homo sapiens reference genome assembly (hg38) using Star version 2.6. The STAR option –outFilterMultimapNmax was set to 1 to allow only uniquely mapped reads.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Gencode annotations (V39).
Assembly: hg38
Supplementary files format and content: RawCounts

source_name: Peripheral Blood CD4 T Cell

growth_protocol: Peripheral blood mononuclear cells (PBMC) were obtained from venous blood of the healthy female donor by density gradient separation using Lymphoprep Density Gradient Media and Sepmate PBMC Isolation Tubes Tubes (StemCell Technologies, 85450). CD4 T cells were then purified using negative magnetic selection via EasySep kit (Stemcell Technologies, Cat#17952). CD4 T cells were plated with Dynabeads Human T-Activator CD3/CD28 (Gibco Cat#11161D) and stimulated for 4, 16, 48, or 120hrs before RNA extraction for sequencing.

extract_protocol:
Activated cells were lysed in well with subsequent Dynabead removal. Total cellular RNA was extracted and purified using RNeasy Plus Mini Kit (Qiagen, 74134) following the manufacturer’s protocol with addition of on-column DNase digestion. High quality RNA was shipped to the HudsonAlpha Institute for Biotechnology for library construction (RIN>9 shipped, all RIN>8 measured directly prior to library construction).
Libraries were prepared by the HudsonAlpha Institute for Biotechnology according to an in-house protocol using NEB PolyA RNA-Seq library prep.

treatment_protocol: CD4 T cells were stimulated with anti-CD3/CD28 Dynabeads at a bead:cell ratio of 1:1 (4, 16, and 48hr) or 3:1 (120hr) for the indicated times prior to RNA extraction. No additional cytokines or stimulants were added during this time. Cells stimulated for 120hrs were split  on day 2 of stimulation with 50% new media added.

value: Peripheral Blood CD4 T Cell

value: female

tag: age

value: 24 years

tag: activation status

value: activated

tag: activation time_point


title: HMC-1 Input

extract_protocol:
Human lens epithelia were collected during standard cataract surgery, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
The m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Novaseq instrument with 150bp paired-end reads.

value: lens capsule

tag: subject status

value: highly myopic cataract (HMC) patient

value: input


title: FLT3 ITD4

description: FLT3 ITD4

value: osteoclasts from CD11b+ BM

value: FLT3 ITD


title: MS3a_NAWM_rep4

value: NAWM/PPWM


title: A062

description: Copy number profiling of patient A062, FFPE tumor tissue

value: Colon Adenocarcinoma


title: HMC-3 Input


title: A056

description: Copy number profiling of patient A056, FFPE tumor tissue

value: Intra-hepatic colangiocarcinoma


title: A061

description: Copy number profiling of patient A061, FFPE tumor tissue

value: High grade serous ovarian carcinoma


title: FLT3 ITD Ptprc KO2

description: FLT3 ITD Ptprc KO2

value: FLT3 ITD Ptprc KO


title: MS3a_RIM_rep4

value: lesion rim


title: MS3a_NAWM_rep3

value: Brain, MS Autopsie


title: Mid-activated CD4 T cells (16hr)

tag: Sex

value: 16 hr


title: ARC-1 Input

value: age-related cataract (ARC) patient


title: MS3a_RIM_rep1

value: CD68 positive


title: A059

description: Copy number profiling of patient A059, FFPE tumor tissue

value: Non smal cells lung cance


title: A053

description: Copy number profiling of patient A053, FFPE tumor tissue

value: Cervical adenosquamous Carcinoma


title: MS3b_NAWM_rep1


title: Early activated CD4 T Cells (4hr)

value: Peripheral Blood CD4 T Cell

value: female

value: 24 years

value: activated

value: 4 hr


title: FLT3 ITD Ptprc KO1

description: FLT3 ITD Ptprc KO1

value: osteoclasts from CD11b+ BM


title: H358, Mock

city: Taichung

first: Jian-Wei

last: Chen

address: 145 Xingda Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: National Chung Hsing University

data_processing:
Trimmomatic program version 0.38 was used to filter out the low-quality bases and the adapter sequences in the raw data.
The HISAT2 program version 2.2.1 was used to align the filtered reads with the GRCh38 reference genome.
The featureCounts program version 2.0.0 was employed to quantify the transcript abundance and to normalize by the transcript per million (TPM) procedure.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: All lung cancer cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA quantification was checked using SimpliNano™-Biochrom Spectrophotometers (Biochrom, MA, USA).
Sequencing libraries were generated using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland). Synthesis of first strand cDNA using random hexamer primers. After generating double-stranded cDNA (dscDNA), in order to preferentially select cDNA fragments with a length of 300-400 bp, the library fragments were purified with KAPA Pure Beads system (KAPA Biosystems, Roche, Basel, Switzerland).

value: Non-small cell lung cancer

value: WT


title: MS3a_RIM_rep3


title: A057

description: Copy number profiling of patient A057, FFPE tumor tissue

value: Pancreatic carcinoma


title: Blasting CD4 T cells (48hr)

value: 48 hr


title: MS3a_RIM_rep2

value: lesion rim


title: Ptprc KO4

description: Ptprc KO4

value: Ptprc KO


title: A051

description: Copy number profiling of patient A051, FFPE tumor tissue

value: Endometrial carcinoma


title: FLT3 ITD3

description: FLT3 ITD3

value: FLT3 ITD


title: MS3b_RIM_rep1

value: Brain, MS Autopsie

value: CD68 positive


title: Ptprc KO2

description: Ptprc KO2


title: Hi-C, sgo1Δ - Tension

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Fastq reads aligned to S.cerevisiae Sc3 using HiC-Pro v3.1.0 , bowtie2 v2.4.2 (--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder), removing singleton, multi hit, MAPQ<10 and duplicated reads.
Valid interaction pairs were converted into the .cool contact matrix format using cooler v0.9.3 (1 kb resolution)
Matrixes balanced with cooler using Iterative correction
Assembly: S.cerevisiae Sc3
Supplementary files format and content: Cooler .cool matrix 1kb binned, balanced with iterative correction

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Cells were diluted to OD(600)=0.2 and arrested G1 with alpha factor for 3 hours, then released into a metaphase arrest by depletion of Cdc20 for 2 hours. "No tension" condition included addition of nocodazole and benomyl, "Tension" condition did not.

extract_protocol:
Lysates were prepared by grinding the frozen pellet in a chilled mortar with a pestle for 15 minutes and 1/10th of the initial pellet weight (~0.5 g) was taken for further processing. Restriction enzyme digestion (DpnII), filling-in, ligation, crosslink reversal, DNA concentration and purification and biotin removal were carried out as described in Schalbetter et al. (2018) doi: https://doi.org/10.1101/442038. DNA was then fragmented on a Bioruptor Plus sonication device (Diagenode) for a total of 2x 30 cycles 30 seconds on/off at High setting.
DNA end repair and A-tailing using T4 DNA polymerase, T4 Polynucleotide Kinase and Klenow fragment DNA polymerase I were carried out as in Schalbetter et al., 2018. Hi-C libraries were fractionated using Ampure XP beads as previously described in Belton et al. (2015) DOI: 10.1101/pdb.prot085209. Biotin pull-down, adapter ligation (NextFlex, Bioo Scientific) and sequencing (EMBL Core Genomics Facility, Heidelberg, Germany) were carried as in Schalbetter et al. (2018) doi: https://doi.org/10.1101/442038.
NextSeqHigh-40 PE

treatment_protocol: Cells were fixed and lysed as in Belton & Dekker (2015) DOI: 10.1101/pdb.prot085209. Briefly, 200 ml of cells at OD~0.6 carrying pMET-CDC20 were arrested in metaphase at 25 ˚C in the presence and absence of tension as described above, fixed with 3% formaldehyde for 20 minutes at 25 ˚C at 250 rpm and the reaction was quenched for 5 minutes by the addition of 0.35 M glycine (final concentration). Cells were washed with cold water, resuspended in 5 ml 1x NEBuffer 2 and frozen in liquid nitrogen.

value: yeast cells

tag: target

tag: cell cycle_stage

value: Metaphase

tag: strain

value: tension


title: MS16a_NAWM_rep4

city: Münster

first: Carolin

last: Walter

value: NAWM/PPWM


title: A055

description: Copy number profiling of patient A055, FFPE tumor tissue

value: Colon Adenocarcinoma


title: MS3b_NAWM_rep2


title: Hi-C, ycg1-4A - Tension


title: A549, TRIM8

tag: cell line

value: lung carcinoma

value: TRIM8 overexpression


title: FLT3 ITD2

description: FLT3 ITD2

value: osteoclasts from CD11b+ BM


title: FLT3 ITD1

description: FLT3 ITD1


title: A052

description: Copy number profiling of patient A052, FFPE tumor tissue

value: Lung Adenocarcinoma


title: Hi-C, Wild type - Tension

value: Wild type

tag: treatment


title: Hi-C, sgo1-2A - Tension


title: MS16a_NAWM_rep1


title: MS3b_RIM_rep2


title: R31_hASAP1_si4_Tra_repB

city: bethesda

first: Jack

last: Shern

address: 10 Center drive

institute: NCI

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome using STAR 2.5.1
fragments per kilobase of exon per million mapped fragments (FPKM) were quantified using the Partek E/M model
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

source_name: RD cells

growth_protocol: RD cells were cultured in high glucose DMEM with 10% FBS and Pen/Strep/Glutamine

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA was isolated from RD cells transfected with control siRNA or ASAP1 siRNA, 48 hours later the transfected cells were treated with DMSO or trametinib for an additional 2 or 3 days.

value: rhabdomyosarcoma

tag: transfected with

value: ASAP1 siRNA

value: trametinib


title: CL1-0, TRIM8

value: lung adenocarcinoma


title: Ptprc KO3

description: Ptprc KO3

value: Ptprc KO


title: CL1-0, Mock

value: WT


title: Ptprc KO1

description: Ptprc KO1


title: MS16a_NAWM_rep3

address: Domagkstraße 9

tag: tissue

value: Brain, MS Autopsie

value: CD68 positive


title: H358, TRIM8

value: Non-small cell lung cancer


title: WT4


title: A549, Mock


title: MS16a_NAWM_rep2


title: WT2


title: WT3


title: Hi-C, sgo1Δ - No tension

value: yeast cells

value: Metaphase

value: no tension


title: R30_ctrl_si5_Tra_repB

value: control siRNA


title: MS16a_RIM_rep4

value: lesion rim


title: Hi-C, ycg1-4A - No tension


title: MS16a_RIM_rep3


title: R29_ctrl_si4_Tra_repB


title: Hi-C, sgo1-2A - No tension


title: Prickle1 f/f

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: 10x Genomics Chromium Single Cell Gene Expression data

data_processing:
The data was analyzed using the 10x Genomics Chromium Single Cell software suite (cellranger-6.1.1).
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the mouse reference (refdata-gex-mm10-2020-A) and analyzed using "cellranger count".
Assembly: mm10
Supplementary files format and content: cellranger generated unfiltered feature-barcode matrix file.

source_name: uterus

extract_protocol:
Uteri were processed by mincing the tissue and digesting in DMEM (Gibco, Waltham, MA), 10% FBS (Atlanta Biologicals, Flower Branch, GA), 1.5mg/ml collagenase (Gibco, Waltham, MA), and 2400U of DNaseI (NEB, Ipswich, MA) for 5 hours in a shaking water bath at 37°C. After digestion, cells were centrifuged at 300g for 5 minutes and treated with ACK lysis buffer followed by two washes with 1X PBS and 2% FBS. Cells were passed through a 100um cell strainer and resuspended in 1X PBS and 2% FBS. Cells were passed through a 40um cell strainer and resuspended in 1X PBS and 2% FBS.
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).

value: uterus

value: female

value: C57BL/6J wild-type


title: Prickle1 f/f Ltf-cre


title: R28_hASAP1_si17_DMSO_repB

value: rhabdomyosarcoma

value: DMSO


title: R32_hASAP1_si17_Tra_repB

value: ASAP1 siRNA

value: trametinib


title: Normal_colon_organoid_scRNA-seq

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

country: South Korea

institute: KAIST

description:
Library name: Normal
10x genomics

data_processing:
We processed single cell RNA seq data using CellRanger version 6.0.0 using default parameters.
We aligned data to the hg38 reference genome.
Assembly: hg38
Supplementary files format and content: h5 format files

source_name: Colon

extract_protocol:
Single cells were obtained form normal colon and colon cancer organoids.
10x genomics library (chemistry version 3, 3 prime seq)

value: Colon

value: Organoid


title: Elf-1 KO, replicate 1, scRNAseq

city: Zhengzhou

first: Peng

last: Wang

address: Science Avenue

institute: Zhengzhou University

description: GEXSCOPE

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope(https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 (Ref) to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a (Ref) to map reads to the reference genome GRCm38 (ensembl version 92 annotation). UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 (Ref) software, and used to generate expression matrix files for subsequent analysis.
Assembly: GRCm38
Supplementary files format and content: matrix

extract_protocol:
For isolation of colon cells, proximal, distal colon, and rectum were collected from DSS-treated WT and   Elf-1-/- mice mice.Intestines were opened longitudinally and washed to remove fecal content with cold PBS, then placed into the GEXSCOPE Tissue Preservation Solution (Singleron Biotechnologies) and transported at 2-8 °C. All tissues were cut into small pieces (1-2 mm3) and digested for 15 min at 37 °C in 2 mL GEXSCOPE Tissue Dissociation Solution (Singleron Biotechnologies). Subsequently, cells were passed through a 40-μm cell strainer and washed in PBS.
Colonic cells were  pooled for scRNA-seq from colon tissues of three mice of each group (DSS-treated WT and Elf-1-/- mice). Cells were loaded into GEXSCOPE Single Cell Microchip (Singleron) and scRNA-seq libraries were constructed according to protocol from GEXSCOPE Single-Cell RNA Library Kit (Singleron). The libraries were finally sequenced with 150 bp paired end on the Illumina Novaseq 6000 platform with a sequencing depth of at least 100,000 reads per cell.

value: 8-10 weeks old


title: MS9_NAWM_rep3

data_processing:
*library strategy: Spatial Transcriptomics
All raw fastq files were processed with the Nanostring GeoMxNGSPipeline v2.3.3.10, and counts per gene were exported as Nanostring DCC files per sample.
Assembly: hg38
Supplementary files format and content: Nanostring GeoMx DCC files with read counts per gene

source_name: Brain, MS Autopsie

value: Brain, MS Autopsie

value: CD68 positive

value: NAWM/PPWM


title: Hi-C, Wild type - No tension

value: yeast cells

value: Metaphase

value: Wild type


title: WT1

value: osteoclasts from CD11b+ BM

value: WT


title: R24_hASAP1_si17_Tra_repB


title: R27_hASAP1_si4_DMSO_repB


title: Sample 3, WT replicate 2, scRNAseq

city: Boston

first: Celine

last: Santiago

state: Massachusetts

address: 210 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

description:
Library name: Sample 3
10x Genomics

data_processing:
Alignment, mapping, and quality control was performed using the 10x genomics cell ranger pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dorsal root ganglia

extract_protocol:
Dorsal root ganglia from segmental levels C2 and below were dissected and dissociated to obtain neurons for single cell RNA sequencing analysis. Sensory ganglia were dissociated in 40 units papain (Worthington LK003178), 4 mg/ml collagenase (Worthington LS004176), 10 mg/ml BSA, 1 mg/ml hyalurdonidase, 0.6 mg/ml DNase in DMEM:F12 (Gibco #11330-032) + 1% pen/strep + 12.5 mM glucose for 25 min at 37 °C. Digestion was quenched using 20 mg/ml ovomucoid (trypsin inhibitor), 20 mg/ml BSA in DMEM:F12 + 1% pen/strep + 12.5 mM glucose. Ganglia were gently triturated with fire-polished glass pipettes (opening diameter of approx. 150–200 μm). Neurons were then passed through a 70-μm filter to remove cell doublets and debris. Neurons were pelleted and washed 4 times in 20 mg/ml ovomucoid (trypsin inhibitor), 20 mg/ml BSA in DMEM:F12 + 1% pen/strep + 12.5 mM glucose followed by 2× washes with DMEM:F12 + 1% pen/strep + 12.5 mM glucose all at 4 °C. After washing, cells were resuspended in 45 μl of DMEM:F12 + 1% pen/strep + 12.5 mM glucose.  ~8000-10000 dissociated cells from DRG were loaded per 10x run (10x genomics chromium single cell kit, v3)
library preparation were performed according to manufacturer's instructions (10x genomics chromium single cell kit, v3)

value: Dorsal root ganglia

value: sensory neuron from DRG

value: Control

tag: batch

value: polyA RNA


title: Tumor_colon_organoid_scRNA-seq

description:
Library name: Tumor
10x genomics


title: MS16a_RIM_rep1

value: lesion rim


title: MS9_NAWM_rep2


title: R26_ctrl_si5_DMSO_repB

value: rhabdomyosarcoma

value: control siRNA

value: DMSO


title: femoral condyle, female bipedal mice with bilateral ovariectomy at 22 weeks of age, scRNAseq

city: Chengdu

first: Yuan

last: Liu

state: Sichuan

address: No. 37 Guoxue Lane, Wuhou District, Chengdu City, Sichuan Province

institute: SiChuan University West China Hospital

data_processing:
Count data were imported into the Seurat single‐cell analysis software (v4.1.3; https://github.com/satijalab/seurat), and quality control of sequenced libraries was performed to remove outlier cells and genes. Seurat was used to perform downstream analysis following the standard pipeline using cells with more than 250 genes, and expressing < 10% mitochondrial genes were retained, resulting in 28158 genes × 65491 cell matrix for further analysis.
Assembly: mm9
Supplementary files format and content: tab-delimited txt file includes row counts for each sample

source_name: femoral condyle

extract_protocol:
Ten femoral condyle tissue, excluding the growth plate, was isolated from the distal epiphyseal line of hindlimbs of 5 mice in each group at 22 weeks of age. Then the femoral condyles tissues were washed in ice-cold RPMI1640, and dissociated using Collagenase Ⅱ (Sigma, V900892-100MG) and DNase Ⅰ (Sigma 9003-98-9). Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Solarbio R1010) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albumin. The CD45-positive cells were selected by flow cytometric sorting, and the CD45-positive and negative cells were mixed in a ratio of 1:1 before the examination.
Single-cell RNA-Seq libraries were prepared using SeekOne® Digital Droplet Single Cell 3’ library preparation kit (SeekGene Catalog No. K00202). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then added to the sample well in SeekOne® chip. Subsequently Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in chip. After emulsion droplet generation reverse transcription were performed at 42℃ for 90 minutes and inactivated at 80℃ for 15 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index. The indexed sequencing libraries were cleanup with SPRI beads, quantified by quantitative PCR (KAPA Biosystems KK4824) and then sequenced on illumina NovaSeq 6000 with PE150 read length.

value: femoral condyle


title: R23_hASAP1_si4_Tra_repB

value: ASAP1 siRNA

value: trametinib


title: MS16a_RIM_rep2

value: Brain, MS Autopsie

value: CD68 positive


title: MS9_NAWM_rep4

value: NAWM/PPWM


title: R25_ctrl_si4_DMSO_repB


title: Sample 4, KO replicate 2, scRNAseq

description:
Library name: Sample 4
10x Genomics

tag: genotype

value: KO


title: femoral condyle, female mice with bilateral ovariectomy at 22 weeks of age, scRNAseq


title: WT, replicate 1, scRNAseq

description: GEXSCOPE

value: Colon

value: 8-10 weeks old


title: R22_ctrl_si5_Tra_repB

tag: cell type


title: MS9_RIM_rep3

tag: location


title: R21_ctrl_si4_Tra_repB


title: MS9_NAWM_rep1


title: R20_hASAP1_si17_DMSO_repB


title: 3minus

city: Heidelberg

first: Jiří

last: Koubek

address: INF 345

department: ZMBH

institute: Heidelberg University

description: RNA was denatured at 95 C for 2 min. RNA was refolded  and incubated for 2 min at 30 C, then quenched by adding beta-mercaptoethanol (BME)

library_source: other

data_processing:
Paired-end sequencing reads were first merged using BBMerge and PCR duplicates were removed with Dedupe. BBDuk was used to remove adaptors and trim the 10N UMI sequences.
Reads were then aligned with STAR using the following parameters: -- alignSJoverhangMin 999, -- alignIntronMax 1, -- alignIntronMin 999
Mismatches to the reference sequence were labeled with MD tags using the SAMtools calmd function.
The coverage and mutation rate for each position were calculated and averaged within replicates using a house-developed script. The sequences with a coverage of < 400 reads were removed from further analysis.
For each sequence, the mutation rates on A/C positions were normalized to a 0-1 scale, while U/G positions were not considered
Assembly: "twist.fasta", custom genome based on synthetic sequences
Supplementary files format and content: "combined_mutation_coverage.csv", contains  sequence name, base, coverage rate, and mutation rate from three replicates

molecule: other

source_name: synthetic pool

growth_protocol: T7 RNA polymerase transcribed RNA

extract_protocol:
RNAs were purified via ethanol precipitation and reverse-transcribed using TGIRT-III (InGex)
The resulting cDNA was gel purified and a 5′ adaptor was ligated.

value: synthetic pool

value: Replicate 3

value: refolded RNA, no DMS added

value: DMS-


title: R19_hASAP1_si4_DMSO_repB


title: Sample 2, KO replicate 1, scRNAseq

description:
Library name: Sample 2
10x Genomics

value: Dorsal root ganglia

value: sensory neuron from DRG

value: polyA RNA


title: MS9_RIM_rep4

value: lesion rim


title: Sample 1, WT replicate 1, scRNAseq

description:
Library name: Sample 1
10x Genomics

value: Control


title: 2denatured

description: RNA was denatured at 95 C for 2 min. DMS  was added to the RNA solution, then quenched by adding beta-mercaptoethanol (BME)

value: Replicate 2

value: denatured control RNA, DMS added

value: denatured


title: R16_hASAP1_si17_Tra_repA

value: rhabdomyosarcoma

value: ASAP1 siRNA

value: trametinib


title: femoral condyle, female bipedal mice at 22 weeks of age, scRNAseq

value: femoral condyle


title: femoral condyle, female normal mice at 22 weeks of age, scRNAseq


title: MS9_RIM_rep2

value: Brain, MS Autopsie

value: CD68 positive


title: 3plus

description: RNA was denatured at 95 C for 2 min. RNA was refolded  and DMS  was added to the folded RNA solution and allowed for 2 min incubation at 30 C, then quenched by adding beta-mercaptoethanol (BME)

value: synthetic pool

value: Replicate 3

value: refolded RNA, DMS added

value: DMS+


title: femoral condyle, male bipedal mice at 22 weeks of age, scRNAseq


title: MS9_RIM_rep1


title: 2-Nab-PTX+Anti-PD-L1, Replicate2, RNA-seq

city: Beijing

first: Yuanyuan

last: Zhang

state: Beijing

address: Panjiayuan nanli #17, Chaoyang District

department: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description:
2-Nab-PTX+Anti-PD-L1_Rep2
Mm_bulk.counts.xls

data_processing:
Demultiplexing, barcode processing, alignment, gene counting, and the generation of raw count matrix were performed by the Cell Ranger toolkit (version 3.1.0)
Assembly: GRCh38, mm10
Supplementary files format and content: Excel file, and matrix files enclosed in RDS

source_name: Breast

extract_protocol:
Tumor biopsy samples were first stored in RNAlater RNA stabilization reagent (QIAGEN) after collection and kept on ice to avoid RNA degradation. Samples were then collected in the RPMI-1640 medium (Gibco), and enzymatically digested with gentle MACS Tumor Dissociation Kit (Miltenyi Biotec) for 60 min on a rotor at 37 °C according to the manufacturer’s protocol. The dissociated cells were next passed through a 40-μm cell-strainer (BD) in the RPMI-1640 medium (Invitrogen) with 10% FBS until uniform cell suspensions were obtained. Subsequently, the suspended cells were passed through cell strainers and centrifuged at 400 g for 10 min. Red blood cells were removed via the same procedure described above. After washing twice with 1x PBS (Invitrogen), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 5’ Kit from 10x Genomics, following the manufacturer’s instructions; Bulk RNA-seq libraries were constructed in Sequanta Technologies Co., Ltd at Shanghai.

value: Breast

value: Total cells

tag: group

value: Post-treatment

value: Nab-paclitaxel plus Anti-PD-L1 antibody


title: R14_ctrl_si5_Tra_repA

state: MD

value: control siRNA


title: R18_ctrl_si5_DMSO_repB

value: DMSO


title: R13_ctrl_si4_Tra_repA


title: MS3a_NAWM_rep1

value: NAWM/PPWM


title: 3denatured

value: denatured control RNA, DMS added

value: denatured


title: 2plus

value: Replicate 2


title: femoral condyle, male normal mice at 22 weeks of age, scRNAseq

value: femoral condyle


title: 2-Nab-PTX+Anti-PD-L1, Replicate1, RNA-seq

description:
2-Nab-PTX+Anti-PD-L1_Rep1
Mm_bulk.counts.xls


title: C48/80 + Anti-PD-L1, Replicate2, RNA-seq

description:
C48/80 + Anti-PD-L1_Rep2
Mm_bulk.counts.xls

value: Compound 48/80 plus Anti-PD-L1 antibody


title: C48/80 + Anti-PD-L1, Replicate3, RNA-seq

description:
C48/80 + Anti-PD-L1_Rep3
Mm_bulk.counts.xls


title: R17_ctrl_si4_DMSO_repB

value: rhabdomyosarcoma


title: 1minus

value: synthetic pool

value: Replicate 1

value: refolded RNA, no DMS added

value: DMS-


title: 2minus


title: C48/80 + Anti-PD-L1, Replicate1, RNA-seq

description:
C48/80 + Anti-PD-L1_Rep1
Mm_bulk.counts.xls

value: Breast


title: RPMI8226, C, ChIP-seq

city: Pamplona

first: Nahia

last: Gomez-Echarte

address: Avenida Pio XII, 55

country: Spain

institute: CIMA

description: ChIPseq

data_processing:
The reads were aligned to the human genome hg38 (GRCh38.p13) for all the samples.
RNA-seq: differential gene expression analysis was performed using DESeq2 package in R Studio.
ATAC-seq and ChIP-seq: After low quality and duplicated reads removal, peaks were determined using MACS2 (q-value 0.01, and p-value 0.001 for ATAC-seq and 10-9 for ChIP-seq) and sample specific regions and constant rows were removed. Then, paired wise analysis comparing the control samples with the treated ones in each cell line per separate.
Assembly: GRCh38.p13
Supplementary files format and content: RNA-seq: Text file containing raw counts of all samples included in the study.
Supplementary files format and content: ATAC-seq and ChIP-seq: excel file with chromosome regions and LFC for each MM cell line compared to the matched control (CellLine_JQ1 vs CellLine_Ctrol)

growth_protocol: MM cell lines were maintained in RPMI-1640 medium containing L-Glutamine supplemented with 1% of penicillin-treptomycin, 2% HEPES Buffer and 20% of Fetal Bovine Serum.

extract_protocol:
RNA was isolated with the MagMAX mirVana total RNA Isolation kit (applied biosystems). ChIP-seq and ATAC-seq protocols were performed as described in Ordoñez, R et al (Genome Res, 2020).
RNA-seq library was prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina). Libraries for ChIP-seq and ATAC-seq were performed as described in Ordoñez, R et al (Genome Res, 2020).

treatment_protocol: JQ1 (Selleck, S7110) resuspended in DMSO was added to cell plates resulting in a final concentration of 1µM. For the negative control of the experiments, DMSO was diluted in PBS in the same way as for the compounds in order to reach equal volumes of DMSO in all conditions.

value: Multiple Myeloma

value: WT

tag: chip antibody

value: H3K27ac (C15410196 , Diagenode)


title: R12_hASAP1_si17_DMSO_repA

value: ASAP1 siRNA


title: UC_5

city: 南京市

first: zhen

last: xu

institute: 南京鼓楼医院

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: ASM18296v3
Supplementary files format and content: Excel file contains fpkm and counts for all samples

organism: Candida albicans

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

value: yeast cell

tag: individual

tag: disease state

value: Ulcerative colitis


title: 2-Nab-PTX+Anti-PD-L1, Replicate3, RNA-seq

description:
2-Nab-PTX+Anti-PD-L1_Rep3
Mm_bulk.counts.xls

value: Total cells

value: Post-treatment

value: Nab-paclitaxel plus Anti-PD-L1 antibody


title: R15_hASAP1_si4_Tra_repA

value: trametinib


title: 1plus

value: refolded RNA, DMS added

value: DMS+


title: Nab-PTX+Anti-PD-L1, Replicate3, RNA-seq

description:
Nab-PTX+Anti-PD-L1_Rep3
Mm_bulk.counts.xls


title: KMS-12, JQ1, ChIP-seq

description: ChIPseq

value: 1microM JQ1 for 72h


title: KMS-12, C, ChIP-seq

description: ChIPseq

value: DMSO


title: KMS-11, JQ1, ChIP-seq

description: ChIPseq


title: UC_2


title: 1denatured

value: synthetic pool

value: Replicate 1

value: denatured control RNA, DMS added

value: denatured


title: R7_hASAP1_si4_Tra_repA

value: rhabdomyosarcoma


title: UC_1


title: Nab-PTX+Anti-PD-L1+DSCG, Replicate3, RNA-seq

description:
Nab-PTX+Anti-PD-L1+DSCG_Rep3
Mm_bulk.counts.xls

value: Breast

value: Nab-paclitaxel plus Anti-PD-L1 antibody plus DSCG


title: Healthy_4

value: yeast cell

value: healthy control


title: Nab-PTX+Anti-PD-L1, Replicate1, RNA-seq

description:
Nab-PTX+Anti-PD-L1_Rep1
Mm_bulk.counts.xls

value: Total cells


title: RPMI8226, JQ1, ChIP-seq

description: ChIPseq

value: Multiple Myeloma

value: WT

value: H3K27ac (C15410196 , Diagenode)


title: Nab-PTX+Anti-PD-L1+DSCG, Replicate2, RNA-seq

description:
Nab-PTX+Anti-PD-L1+DSCG_Rep2
Mm_bulk.counts.xls

value: Post-treatment


title: UC_4

value: Ulcerative colitis


title: R11_hASAP1_si4_DMSO_repA

value: ASAP1 siRNA


title: DSCG, Replicate3, RNA-seq

description:
DSCG_Rep3
Mm_bulk.counts.xls

value: DSCG


title: R10_ctrl_si5_DMSO_repA

value: control siRNA

value: DMSO


title: Nab-PTX+Anti-PD-L1+DSCG, Replicate1, RNA-seq

description:
Nab-PTX+Anti-PD-L1+DSCG_Rep1
Mm_bulk.counts.xls


title: RPMI8226, JQ1, ATAC-seq

description: ATACseq

value: 1µM JQ1 for 72h


title: Nab-PTX+Anti-PD-L1, Replicate2, RNA-seq

description:
Nab-PTX+Anti-PD-L1_Rep2
Mm_bulk.counts.xls

value: Nab-paclitaxel plus Anti-PD-L1 antibody


title: R9_ctrl_si4_DMSO_repA

value: rhabdomyosarcoma


title: R8_hASAP1_si17_Tra_repA

value: trametinib


title: DSCG, Replicate2, RNA-seq

description:
DSCG_Rep2
Mm_bulk.counts.xls

value: Breast


title: R6_ctrl_si5_Tra_repA


title: UC_3

value: yeast cell


title: KMS-11, C, ChIP-seq

description: ChIPseq


title: Healthy_3

value: healthy control


title: R4_hASAP1_si17_DMSO_repA


title: Healthy_2


title: RPMI8226, C, ATAC-seq

description: ATACseq


title: Healthy_1


title: Control-3, Replicate3, RNA-seq

description:
Control-3_Rep3
Mm_bulk.counts.xls

value: Total cells

value: Control


title: Healthy_5


title: R3_hASAP1_si4_DMSO_repA


title: R2_ctrl_si5_DMSO_repA


title: KMS-12, JQ1, ATAC-seq

description: ATACseq

value: Multiple Myeloma

value: WT


title: R5_ctrl_si4_Tra_repA


title: Control-3, Replicate2, RNA-seq

description:
Control-3_Rep2
Mm_bulk.counts.xls

value: Post-treatment


title: DSCG, Replicate1, RNA-seq

description:
DSCG_Rep1
Mm_bulk.counts.xls


title: C-TET1KO

city: Shanghai

first: Dan

last: Zhou

address: 131 Dong 'an Road, Xuhui District

institute: Fudan University

data_processing:
Differentially expressed genes were identified using the DESeq2 R package, with those exhibiting a P-value of less than 0.05 considered significant. Gene ontology and pathway enrichment analysis were performed using the clusterProfiler R package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: mES cells

growth_protocol: Mouse ES cells were maintained on 0.1% gelatin-coated plate and cultured in DMEM supplemented with 15% FBS (GIBCO), 2 mM L-glutamine, 0.1 mM non-essential amino acids (GIBCO), 1 mM sodium pyruvate (GIBCO), 0.1 mM 2-mercaptoethanol (Sigma), 1x Pen/Strep, 3 μM CHIR99021, 1 μM PD0325901, and 1000 U/ml mouse LIF (Sigma-Aldrich).

extract_protocol:
Total RNA was extracted from mES cells using the RNAsimple Total RNA Kit (TIANGEN).
The raw paired-end FASTQ files were analyzed following the standard protocol as previously described

treatment_protocol: no

value: mES cells

value: Tet1 KO

value: no


title: R1_ctrl_si4_DMSO_repA

value: control siRNA


title: C-81

value: Tet1KO Tet2 N1300T


title: KMS-12, C, ATAC-seq

description: ATACseq

value: DMSO


title: Control-3, Replicate1, RNA-seq

description:
Control-3_Rep1
Mm_bulk.counts.xls


title: C48/80, Replicate5, RNA-seq

description:
C48/80_Rep5
Mm_bulk.counts.xls


title: C-49


title: KMS-11, C, ATAC-seq

description: ATACseq


title: RPMI8226, JQ1, R2 RNA-seq

description:
RNAseq
RPMI8226_JQ1_Rep2

value: 1microM JQ1 for 72h


title: Con1-input

city: Hefei

first: Yue

last: Zhu

address: The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Assembly: hg38
Supplementary files format and content: xlsx files

source_name: liver

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: liver

value: Human liver cancer cells


title: C48/80, Replicate4, RNA-seq

description:
C48/80_Rep4
Mm_bulk.counts.xls

value: Breast


title: TM3-H3K27ac

institute: The First Affiliated Hospital of Anhui Medical University

value: TM


title: TM2-H3K27ac


title: C-41

value: Tet1 Tet2 DKO


title: B-TET1KO


title: C48/80, Replicate2, RNA-seq

description:
C48/80_Rep2
Mm_bulk.counts.xls

value: Total cells

value: Compound 48/80


title: TM1-H3K27ac


title: C48/80, Replicate3, RNA-seq

description:
C48/80_Rep3
Mm_bulk.counts.xls


title: Con3-H3K27ac


title: KMS-11, JQ1, R2 RNA-seq

description:
RNAseq
KMS11_JQ1_Rep2

value: Multiple Myeloma


title: KMS-12, JQ1, R2 RNA-seq

description:
RNAseq
KMS12_JQ1_Rep2

value: WT


title: KMS-11, JQ1, ATAC-seq

description: ATACseq

value: 1µM JQ1 for 72h


title: KMS-12, C, R2 RNA-seq

description:
RNAseq
KMS12_Ctrol_Rep2


title: B-81

value: mES cells


title: B-41


title: B-49


title: Control-2, Replicate5, RNA-seq

description:
Control-2_Rep5
Mm_bulk.counts.xls

value: Post-treatment

value: Control


title: Con2-H3K27ac


title: Control-2, Replicate4, RNA-seq

description:
Control-2_Rep4
Mm_bulk.counts.xls


title: A-TET1KO

value: Tet1 KO

value: no


title: Con1-H3K27ac

value: DMSO


title: KMS-11, C, R2 RNA-seq

description:
RNAseq
KMS11_Ctrol_Rep2


title: RPMI8226, JQ1, R1 RNA-seq

description:
RNAseq
RPMI8226_JQ1_Rep1

value: 1microM JQ1 for 72h


title: RPMI8226, C, R2 RNA-seq

description:
RNAseq
RPMI8226_Ctrol_Rep2