title: pFC9 with NtBspQI Target Site 3, No NtBspQI (Not Nicked), Transcribed, RnaseH1 Treated, rep1

description:
Library name: Sample 46
pFC9NtBspQITargetSite3_AddNtBspQI_NotNicked_NoSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: bacterial


title: S01 Monocyte, High Salt (190mmol/L NaCl)

status: Public on Sep 26 2025

type: SRA

city: Nashville

first: Ashley

last: Mutchler

address: 1005 Dr. D.B. Todd Jr. Boulevard

country: USA

institute: Meharry Medical College

description:
Library name: Sample 12
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-12_S12

library_source: transcriptomic

data_processing:
Using the R package, the FASTQ data files from the paired-end sequencing analysis were aligned with TopHat 2 for each sample against the human GRCh38 reference genome assembly. Quality control for the RNAseq data occurred during the following stages: 1) RNA quality; 2) raw read data (FASTQ); 3) alignment; 4) gene expression. Quality control for the raw data and alignment were performed using QC3 , and the MultiRankSeq method was used for expression analysis. Raw data false discovery rate (FDR < 0.05) was used to correct for multiple hypothesis testing.
Assembly: human GRCh38
Supplementary files format and content: excel file containing  FPKM values and DESeq2 paired-analysis

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Rneasy Midi Kit (Qiagen) according to manufacturer's protocol
Targeted analysis of polyadenylated transcripts was performed using the Illumina Tru-seq RNA sample prep kit

tag: tissue

value: Peripheral blood

tag: cell type

value: Monocytes

tag: treatment

value: High salt (190 mmol/L NaCl)

tag: batch


title: ALL survivor 129

type: genomic

city: Montréal

first: Daniel

last: Sinnett

state: Québec

address: 3175 Chem. de la Côte-Sainte-Catherine

department: Research Center

country: Canada

institute: CHU Sainte-Justine

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC V1.0 Beadchip using standard Illumina protocol

scan_protocol: standard  protocol for Illumina HiScan

data_processing:
The raw IDAT files were processed into β-values, which quantify DNA methylation levels on a scale from 0 to 1, using the minfi package from Bioconductor in R v4.1.1. The data was then normalized using the preprocessIllumina function in minfi to correct for technical variation. The preprocessing pipeline included several filtering steps: removal of non-specific probes; exclusion of probes with detection p-values greater than 0.05 in more than 25% of samples; elimination of probes located near SNPs (within 10 bp of the CpG site or single base extension) or associated with SNPs having a minor allele frequency above 1%; removal of probes with β-values of 0 or 1 in more than 0.25% of samples; exclusion of non-CpG probes; and filtering out probes located on sex chromosomes. Quality control was performed using standard minfi metrics such as median intensity plots, density distributions, and control probe assessments, with all samples passing QC and included in the final analysis.
normalized betas

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Whole blood

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from blood samples using DNEasy (Qiagen) chemistry and columns. No modification was made to the manufacturer's specifications.

value: Whole blood

tag: Sex

value: Male

tag: age at sample collection


title: F84 neuronal progenitor cell clonal line (RNA-seq)

city: Stanford

first: Christy

last: Luong

state: CA

address: 269 Campus Dr

department: Department of Dermatology

institute: Stanford University School of Medicine

description:
Library name: F84_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

data_processing:
Reads were aligned to an N-masked genome and transcriptome using STAR. Aligned reads were then split using informative SNPs using SNPsplit for allele-specific analysis. We also kept mapped reads that did not undergo SNPsplit to perform non-allele specific analysis. Transcripts are quantified using Salmon and tximport was used to import and summarize transcripts for downstream gene-level analysis.
Assembly: mm10
Supplementary files format and content: tximport_all_withgenes.csv is a output file from tximport that summarizes Salmon output for gene-level analysis from non-allele specific mapped RNA-seq reads. File contains non-allele specific estimated counts, abundances, and gene_names. Columns are the sample names.
Supplementary files format and content: tximport_allele_specific_all_withgenes.csv is a output file from tximport that summarizes  Salmon output for gene-level analysis from allele specific mapped RNA-seq reads. File contains allele-specific estimated counts, abundances, and gene_names. Columns are the sample names.

molecule: polyA RNA

organism: Mus musculus

growth_protocol: NPCs were differentiated from mESCs from 2i+Lif. NPCs were grown on 0.1% gelatin with N2B27 medium with FGF and EGF. F123 mESCs were growon on 0.1% gelatin with N2B27 medium with 2i+Lif

extract_protocol:
RNA was extracted with Trizol and purified using Zymo RNA direct-zol mini prep kit.
total RNA was given to Novogene for directional RNA library prep with polyA enrichment

value: Female

tag: cell line

value: neuronal progenitor cells


title: pFC9 with NtBspQI Target Site 3, No NtBspQI (Not Nicked), Transcribed, rep1

city: DAVIS

first: FREDERIC

last: CHEDIN

address: 1 shields avenue

department: MCB

institute: UC DAVIS

description:
Library name: Sample 44
pFC9NtBspQITargetSite3_AddNtBspQI_NotNicked_NoSSB_Transcribed_reference_sequence.fasta.gz

library_source: genomic

data_processing:
library strategy: Single-molecule R-loop footprinting sequencing (SMRF-seq)
Resulting SMRF-seq fastq files were processed and R-loop footprints were called using the previously published Gargamel pipeline (https://github.com/srhartono/footLoop). R-loops were called using minimum parameters of 50 base pair minimum peak length (-l), at least 20 cytosines present in the R-loop (-w), and cytosine conversion rate (-t) of 55% (high threshold) or 35% (low threshold)
Assembly: all reference sequence used to align the reads is provided
Supplementary files format and content: bed: bed 6 files containing R-loop peaks called with high threshold parameters (-t 55 -w 20 -l 50) or low threshold parameters (-t 35 -w 20 -l50)
Supplementary files format and content: fasta.gz: reference sequence used to align the reads in gzipped FASTA format (linked to the corresponding rep1 sample records)

organism: synthetic construct

source_name: bacterial

growth_protocol: Plasmids were transformed into E. coli DH5α chemically competent cells and single colonies were grown on LB ampicillin agar plates. Single colonies were selected and grown in 300 ml LB culture with 100 µg   / ml of ampicillin in 1 L flasks at either 30° or 37°C overnight with shaking at 200-250 rpm.

extract_protocol:
Negatively supercoiled plasmid substrates were purified by alkaline lysis protocol followed by column cleanup (Qiagen) and eluted into either TE or EB buffer.
Single-Molecule R-loop Footprinting (SMRF-seq) samples were amplified with a combination of forward and reverse primers that each incorporated a unique barcode. The combination of the forward and reverse primer barcodes uniquely identifies each sample within its specific flowcell. Primer binding sequences were designed in Primer3 (10) software and barcodes were generated using a custom Python script. Samples were amplified using Q5U® Hot Start High-Fidelity DNA Polymerase (NEB M0515S) for 25-30 cycles according to the manufacturer’s online protocol. 1-3 μl of bisulfite converted substrate was used for each reaction. In the case that the yield of one reaction was not sufficient, additional reactions using the original bisulfite converted sample were performed and then pooled. The target amplicon size was then purified via agarose gel extraction using BioBasic gel extraction kit (BS654). Sample concentration was quantified via agarose gel electrophoresis against 1kb linear DNA ladder (Thermo Fisher SM0311). SMRT cell PacBio libraries were constructed by the UC Davis DNA Technologies core according to manufacturer’s instructions and sequenced on a PacBio Sequel II instrument. Additional sequencing was performed at the UC Berkeley QB3 sequencing core on a PacBio Revio instrument.

tag: plasmid

value: pFC9 with NtBspQI Target Site 3 Insert

value: Transcribe with T7 RNA Polymerase


title: ALL survivor 128


title: ALL survivor 127


title: M01 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M01_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: S11 Monocyte, Normal Salt (140mmol/L NaCl)

description:
Library name: Sample 11
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-11_S11

value: Normal salt (140 mmol/L NaCl)


title: S10 Monocyte, Normal Salt (140mmol/L NaCl)

description:
Library name: Sample 10
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-10_S10


title: F83 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F83_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 126


title: pFC9 with NtBspQI Target Site 2, Add NtBspQI (Nicked), Transcribed, RnaseH1 Treated, rep1

description:
Library name: Sample 40
pFC9NtBspQITargetSite2_AddNtBspQI_Nicked_NoSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: pFC9 with NtBspQI Target Site 2 Insert

value: Add NtBspQI (nick at site 2), Transcribe with T7 RNA Polymerase, Treat with Rnaseh1 before bisulfite treatment


title: S08 Monocyte, Normal Salt (140mmol/L NaCl)

description:
Library name: Sample 8
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-8_S8


title: S09 Monocyte, Normal Salt (140mmol/L NaCl)

description:
Library name: Sample 9
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-9_S9


title: F81 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F81_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: pFC9 with NtBspQI Target Site 2, Add NtBspQI (Nicked), Untranscribed, rep1

description:
Library name: Sample 36
pFC9NtBspQITargetSite2_AddNtBspQI_Nicked_NoSSB_Untranscribed_reference_sequence.fasta.gz

value: Add NtBspQI (nick at site 2)


title: F82 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F82_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: pFC9 with NtBspQI Target Site 3, No NtBspQI (Not Nicked), Untranscribed, rep1

description:
Library name: Sample 42
pFC9NtBspQITargetSite3_AddNtBspQI_NotNicked_NoSSB_Untranscribed_reference_sequence.fasta.gz


title: ALL survivor 124


title: pFC9 with NtBspQI Target Site 2, No NtBspQI (Not Nicked), Transcribed, RnaseH1 Treated, rep1

description:
Library name: Sample 34
pFC9NtBspQITargetSite2_AddNtBspQI_NotNicked_NoSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: Transcribe with T7 RNA Polymerase, Treat with Rnaseh1 before bisulfite treatment


title: F80 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F80_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: S06 Monocyte, Normal Salt (140mmol/L NaCl)

description:
Library name: Sample 6
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-6_S6


title: pFC9 with NtBspQI Target Site 2, Add NtBspQI (Nicked), Transcribed, rep1

description:
Library name: Sample 38
pFC9NtBspQITargetSite2_AddNtBspQI_Nicked_NoSSB_Transcribed_reference_sequence.fasta.gz

value: Add NtBspQI (nick at site 2), Transcribe with T7 RNA Polymerase


title: pFC9 with NtBspQI Target Site 2, No NtBspQI (Not Nicked), Transcribed, rep1

description:
Library name: Sample 32
pFC9NtBspQITargetSite2_AddNtBspQI_NotNicked_NoSSB_Transcribed_reference_sequence.fasta.gz


title: ALL survivor 125


title: ALL survivor 123


title: S05 Monocyte, Normal Salt (140mmol/L NaCl)

description:
Library name: Sample 5
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-5_S5


title: F79 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F79_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: F78 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F78_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 122


title: pFC9 with NtBspQI Target Site 2, No NtBspQI (Not Nicked), Untranscribed, rep1

description:
Library name: Sample 30
pFC9NtBspQITargetSite2_AddNtBspQI_NotNicked_NoSSB_Untranscribed_reference_sequence.fasta.gz


title: S04 Monocyte, Normal Salt (140mmol/L NaCl)

description:
Library name: Sample 4
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-4_S4


title: F76 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F76_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: S03 Monocyte, Normal Salt (140mmol/L NaCl)

description:
Library name: Sample 3
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-3_S3


title: F73 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F73_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 120


title: pFC9 with NtBspQI Target Site 1, Add NtBspQI (Nicked), Transcribed, rep1

description:
Library name: Sample 26
pFC9NtBspQITargetSite1_AddNtBspQI_Nicked_NoSSB_Transcribed_reference_sequence.fasta.gz

value: pFC9 with NtBspQI Target Site 1 Insert

value: Add NtBspQI (nick at site 1), Transcribe with T7 RNA Polymerase


title: S02 Monocyte, Normal Salt (140mmol/L NaCl)

description:
Library name: Sample 2
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-2_S2

value: Peripheral blood


title: F71 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F71_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: S07 Monocyte, Normal Salt (140mmol/L NaCl)

description:
Library name: Sample 7
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-7_S7

value: Monocytes


title: pFC9 with NtBspQI Target Site 1, Add NtBspQI (Nicked), Untranscribed, rep1

description:
Library name: Sample 24
pFC9NtBspQITargetSite1_AddNtBspQI_Nicked_NoSSB_Untranscribed_reference_sequence.fasta.gz

value: bacterial

value: Add NtBspQI (nick at site 1)


title: ALL survivor 119

value: Whole blood

value: Male


title: F70 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F70_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: Female

value: neuronal progenitor cells


title: ALL survivor 118


title: pFC9 with NtBspQI Target Site 1, No NtBspQI (Not Nicked), Transcribed, RnaseH1 Treated, rep1

description:
Library name: Sample 22
pFC9NtBspQITargetSite1_AddNtBspQI_NotNicked_NoSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz


title: F67 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F67_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: F65 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F65_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: F68 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F68_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: pFC9 with NtBspQI Target Site 1, Add NtBspQI (Nicked), Transcribed, RnaseH1 Treated, rep1

description:
Library name: Sample 28
pFC9NtBspQITargetSite1_AddNtBspQI_Nicked_NoSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: Add NtBspQI (nick at site 1), Transcribe with T7 RNA Polymerase, Treat with Rnaseh1 before bisulfite treatment


title: 2w-b rep 1

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 1

data_processing:
Trimmed for adapter sequences using Trimmomatic-0.36 to trim overrepresented sequences.
Alignment and annotated the raw data to the Homo sapiens NCBI GRCh38 genome using Tophat.
Variance stabilization performed using log2 scaling.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include log2 counts values for each sample

source_name: 2w-b rep 1

growth_protocol: Human skin xenotransplants into SCID/Beige mice: Following ethics approval and informed consent, 1-cm2 skin samples of split-thickness (0.4-mm) were obtained from non-UV-exposed areas of the upper thighs. Aged volunteers were included in this study. The viable human skin samples were xenotransplanted onto immunodeficiency SCID/Beige young mice.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer's protocol.  RNA concentration and quality were determined using a 4200 TapeStation Instrument (Agilent). RNA quantity and quality were measured using a NanoDrop ND-8000 spectrophotometer. Samples with a RIN value greater than 8.0 were used for RNA-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Twelve young mice (2.5±0.4 month) were transplanted with skin from 2 male donors (mean age 82±7). RNA-Seq was employed pre-transplantation and after the first, second and fourth weeks following engraftment. Approximately 1 cm2 of skin tissue was taken with sterile forceps and quickly cut using sterile scalpel blades. Skin was then stored in RNAlater (Thermo Fisher Scientific, USA) for RNA extraction.

value: human skin xenotransplants

tag: recipient mouse transplantation period

value: Week 2 Post-transplantation

tag: recipient mouse strain

value: SCID/Beige

tag: human donor id

tag: gender

tag: donor mean age


title: pFC9 with NtBspQI Target Site 1, No NtBspQI (Not Nicked), Transcribed, rep1

description:
Library name: Sample 20
pFC9NtBspQITargetSite1_AddNtBspQI_NotNicked_NoSSB_Transcribed_reference_sequence.fasta.gz

value: Transcribe with T7 RNA Polymerase


title: 2w-b rep 2

description: replicate 2

source_name: 2w-b rep 2


title: ALL survivor 117


title: ALL survivor 114


title: 4w-a

description: replicate 1

value: Week 4 Post-transplantation


title: pFC9 with NtBspQI Target Site 1, No NtBspQI (Not Nicked), Untranscribed, rep1

description:
Library name: Sample 18
pFC9NtBspQITargetSite1_AddNtBspQI_NotNicked_NoSSB_Untranscribed_reference_sequence.fasta.gz


title: ALL survivor 113


title: ALL survivor 121


title: ALL survivor 115


title: ALL survivor 116


title: ALL survivor 112


title: S8_TCR

city: Oxford

first: Andrew

last: Foers

address: Roosevelt Dr

country: United Kingdom

institute: Kennedy Institute of Rheumatology

description: Library name: OX19_TCR

data_processing:
Sequence reads were mapped using CellRanger multi (version 7.0.0) with the 10x human reference transcriptomes (refdata-gex-GRCh38-2020-A; refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0).
Assembly: refdata-gex-GRCh38-2020-A
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0
Supplementary files format and content: For GEX - (CellRanger barcodes, features and  matrix output files)
Supplementary files format and content: For TCR seq - CellRanger  vdjt_filtered_contig_annotations csv
Library strategy: TCR-seq

source_name: Aqueous humour

extract_protocol:
80-250 µl of aqueous humour was aspirated from the anterior chamber of 11 consenting patients (Supplementary Table 2) presenting at Oxford Eye Hospital with uveitis. Aqueous humour was kept at 4°C for up to 4 hours before processing for single cell RNA sequencing (scRNAseq). Cells were pelleted by centrifugation at 500xg for 5 mins at RT and cell pellets resuspended in 40 µl of 1% BSA/PBS and loaded onto 10X Genomics Chromium Controller (Chip K).
Gene expression and T cell receptor (TCR) sequencing libraries were prepared using the 10x Genomics Single Cell 5’ Reagent Kits v2 (Dual Index) following manufacturer’s protocol (CG000330 Rev B) and stored at -20°C at 10 nM. Libraries were sent to Novogene (Cambridge, UK) and sequenced on the NovaSeq X Plus platform (Illumina, v1.5 chemistry, 150bp paired end).

value: Aqueous humour

tag: type of_uveitis

value: Undifferentiated acute anterior uveitis

value: NEG

tag: infectious or_non-infectious

value: Non-infectious

tag: sampled eye

value: L

tag: clincal cell_score

tag: age

value: F

tag: ethnicity

value: Afro-Caribbean


title: F61 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F61_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

tag: cell type


title: S9_TCR

description: Library name: OX25_TCR

tag: tissue

value: White


title: 1w-b rep 2

description: replicate 2

source_name: 1w-b rep 2

value: Week 1 Post-transplantation

value: Male


title: S11_TCR

description: Library name: OX32_TCR

value: Acute anterior uveitis

value: POS

tag: Sex

value: M


title: F62 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F62_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: Female

value: neuronal progenitor cells


title: F63 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F63_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: S01 Monocyte, Normal Salt (140mmol/L NaCl)

description:
Library name: Sample 1
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-1_S1

value: Peripheral blood

value: Monocytes

tag: genotype

tag: treatment

value: Normal salt (140 mmol/L NaCl)

tag: batch


title: S7_TCR

description: Library name: OX16_TCR

value: Aqueous humour

value: HLA-B57+ acute anterior uveitis

value: R


title: F64 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F64_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

tag: cell line


title: 2w-a rep 2

description: replicate 2

source_name: 2w-a rep 2

value: human skin xenotransplants

tag: recipient mouse transplantation period

value: Week 2 Post-transplantation

tag: recipient mouse strain

value: SCID/Beige


title: ALL survivor 111

value: Whole blood

tag: age at sample collection


title: 2w-a rep 1

description: replicate 1

source_name: 2w-a rep 1

tag: human donor id

tag: gender

tag: donor mean age


title: S10_TCR

description: Library name: OX31_TCR

tag: type of_uveitis

tag: infectious or_non-infectious

value: Non-infectious

tag: sampled eye

value: F

value: White


title: 4w-b

description: replicate 1

value: Week 4 Post-transplantation

value: Male


title: 1w-b rep 1

description: replicate 1

source_name: 1w-b rep 1

value: Week 1 Post-transplantation


title: ALL survivor 110


title: F60 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F60_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: Female

value: neuronal progenitor cells


title: F59 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F59_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: S6_TCR

description: Library name: OX15_TCR

value: Anterior uveitis

value: NEG

value: L

tag: clincal cell_score

tag: age

tag: ethnicity

value: South east asian (Filipino)


title: S5_TCR

description:
Library name: OX14_TCR
OX14 was loaded on the 10X with another sample (OX13). OX13 was a female donor with a much lower cell count. Cells were demultiplexed from processed data files based on SNPs and sex. Cells from OX13 were not included in the paper.

tag: tissue

value: Aqueous humour

value: Undifferentiated acute anterior uveitis

value: R

tag: Sex

value: M

value: South asian


title: ALL survivor 109

tag: cell type

value: Whole blood


title: 1w-a rep 1

description: replicate 1

source_name: 1w-a rep 1

value: human skin xenotransplants

value: SCID/Beige


title: F58 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F58_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 108


title: S4_TCR

description: Library name: OX12_TCR

value: Acute anterior uveitis

value: Non-infectious

value: F

value: African


title: F57 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F57_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: Female

value: neuronal progenitor cells


title: S3_TCR

description: Library name: OX10_TCR

value: POS

value: White


title: ALL survivor 107


title: ALL survivor 106


title: S2_TCR

description: Library name: OX09_TCR

value: Bilateral intermediate uveitis with cystoid macular oedema

value: NEG

value: L


title: F56 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F56_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 105


title: F53 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F53_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: Pre-a rep 2

description: replicate 2

source_name: Pre-a rep 2

value: Pre-transplantation

value: Male


title: S1_TCR

description: Library name: OX07_TCR

value: Aqueous humour

value: Toxoplasmosis posterior uveitis

value: Infectious

value: R


title: ALL survivor 104

value: Whole blood


title: F52 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F52_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: S11_GEX

description: Library name: OX32_GEX

library_source: transcriptomic single cell

data_processing:
Sequence reads were mapped using CellRanger multi (version 7.0.0) with the 10x human reference transcriptomes (refdata-gex-GRCh38-2020-A; refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0).
Assembly: refdata-gex-GRCh38-2020-A
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0
Supplementary files format and content: For GEX - (CellRanger barcodes, features and  matrix output files)
Supplementary files format and content: For TCR seq - CellRanger  vdjt_filtered_contig_annotations csv

value: Acute anterior uveitis

value: Non-infectious

value: M


title: 1w-a rep 2

description: replicate 2

source_name: 1w-a rep 2

value: human skin xenotransplants

value: Week 1 Post-transplantation

value: SCID/Beige


title: F123_mESC_H3K27ac_Ab Biological repliacate 2

description:
Library name: F123_mESC_H3K27ac_Ab_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

data_processing:
Reads were aligned with Bowtie2 with a custom N-masked genome. Reads were then deduplicated and indexed with samtools. For allele-specific analysis, reads were split based on informative SNPs using SNPSplit.
Assembly: mm10
Supplementary files format and content: BigWig files: created using bamCovarage with normalization using RPGC and bin size of 10 Genome 1 is the 129 allele and genome 2 is the CAST allele.

growth_protocol: NPC were ifferentiated from mESCs from 2i+Lif. NPCs were grown on 0.1% gelatin with N2B27 medium with FGF and EGF. mESCs were grown on 0.1% gelatin with 2i+lif medium.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 mins and lysed with nuclear lysis buffer containing NP-40. Chromtain was then sheared with a Covaris. Sonicated chromatin underwent immunoprecipitation with antibody of choice then DNA was purified.
NEB II Ultra DNA library prep kit was used for library prep with the ChIP DNA.

value: male

value: embryonic stem cells

tag: chip-antibody


title: F51 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F51_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: Female

tag: cell line

value: neuronal progenitor cells


title: ALL survivor 103


title: S10_GEX

description: Library name: OX31_GEX

value: POS

value: F

value: White


title: Ch8_NPC_H3K27ac_Ab Biological repliacate 2

description:
Library name: Ch8_NPC_H3K27ac_Ab_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: F50 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F50_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 102

value: Male


title: S9_GEX

description: Library name: OX25_GEX

value: Aqueous humour

value: Undifferentiated acute anterior uveitis

value: NEG

value: L


title: Ch1_NPC_H3K27ac_Ab Biological repliacate 2

description:
Library name: Ch1_NPC_H3K27ac_Ab_R2
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: Pre-b rep 2

description: replicate 2

source_name: Pre-b rep 2

tag: recipient mouse transplantation period

value: Pre-transplantation


title: F44 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F44_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: F123 mouse embryonic stem cell (bisulfite-seq) biol rep 2

description:
Library name: F123_mESC_methyl_R2
bisulfite-seq on mESCs with PE 150 and ~15 million PE reads

data_processing:
Reads were aligned and deduplicated using an N-masked custom genome and Bismark in allele-specific mode. Aligned reads were then split using SNPsplt on informative SNPs. Resulting bam files were they visualized using bamCoverage to create BigWig files.
Assembly: mm10
Supplementary files format and content: BigWig files were created using bamCoverage from allele-specific bam files using RPGC and a bin of 10. Genome 1 the 129 allele and genome 2 is the CAST allele.

extract_protocol:
Genomic DNA was extracted using genomic lysis buffer followed by phenol chloroform purification and isoporanol precipitation.
Library was constructed using illumina's TruSeq Methyl Epic Capture library prep kit.


title: F43 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F43_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 101

value: Whole blood


title: S7_GEX

description: Library name: OX16_GEX

value: HLA-B57+ acute anterior uveitis

value: Non-infectious

value: R


title: Pre-b rep 1

description: replicate 1

source_name: Pre-b rep 1

value: human skin xenotransplants

tag: recipient mouse strain

value: SCID/Beige


title: Pre-a rep 1

description: replicate 1

source_name: Pre-a rep 1


title: ALL survivor 99

value: Female

tag: age at sample collection


title: mE6 neuronal progenitor cell clonal line (bisulfite-seq) biol rep 2

description:
Library name: mE6_NPC_methyl_R2
bisulfite-seq on NPC with PE 150 and ~15 million PE reads

value: Neuronal progenitor cells


title: Ch8 neuronal progenitor cell clonal line (bisulfite-seq) biol rep 2

description:
Library name: Ch8_NPC_methyl_R2
bisulfite-seq on NPC clonal line with PE 150 and ~15 million PE reads


title: S5_GEX

description:
Library name: OX14_GEX
OX14 was loaded on the 10X with another sample (OX13). OX13 was a female donor with a much lower cell count. Cells were demultiplexed from processed data files based on SNPs and sex. Cells from OX13 were not included in the paper.

value: M

value: South asian


title: Ch1 neuronal progenitor cell clonal line (bisulfite-seq) biol rep 2

description:
Library name: Ch1_NPC_methyl_R2
bisulfite-seq on NPC clonal line with PE 150 and ~15 million PE reads


title: ALL survivor 98


title: F40 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F40_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: neuronal progenitor cells


title: S6_GEX

description: Library name: OX15_GEX

value: Anterior uveitis

value: F

value: South east asian (Filipino)


title: F39 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F39_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: S4_GEX

description: Library name: OX12_GEX

value: Aqueous humour

value: Acute anterior uveitis

value: NEG

value: African


title: F36 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F36_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: S3_GEX

description: Library name: OX10_GEX

value: POS

value: L

value: White


title: ALL survivor 96

value: Whole blood


title: ALL survivor 97

value: Male


title: CTL rep4

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

data_processing:
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:3 TRAILING:10 MINLEN:25
paired-end reads were aligned to the mm10 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16  --quantMode GeneCounts
Assembly: mm10
Supplementary files format and content: tab delimited file with raw read count per gene.

source_name: Thy1.2+ splenocytes

growth_protocol: Cells were directly processed for RNA isolation

extract_protocol:
RNA was extracted by the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were isolated by fluoresecence-activated-cell-sorting (FACS)

value: Thy1.2+ splenocytes

tag: genotype

value: MiG-empty


title: F31 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F31_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: Female


title: S2_GEX

description: Library name: OX09_GEX

value: Bilateral intermediate uveitis with cystoid macular oedema

value: Non-infectious

value: M


title: ALL survivor 95


title: CTL rep3


title: ALL survivor 94


title: mE6 neuronal progenitor cell clonal line (H3K27ac HiCHIP)

description:
Library name: mE6_NPC_H3K27ac_HiChIP
Protein-enriched long-range contact

data_processing:
Reads were passed through the Hi-C Pro pipeline in allele-specific mode for alignment, pairing, and filtering. FitHiChIP was used to call significant loops from .ValidPair files and to create visualization files.
Assembly: mm10
Supplementary files format and content: *.allValidPairs: aligned, paired, and filtered output file from HiC-Pro Pipeline and G1 is 129 allele and G2 is Cast allele.
Supplementary files format and content: *bedpe: output file for visualizing signficant interactions on IGV using loop called FitHiChIP. File contains significant loops with FDR set to 0.1.
Library strategy: HiChIP

growth_protocol: Differentiated from mESCs from 2i+Lif. NPCs were grown on 0.1% gelatin with N2B27 medium with FGF and EGF.

extract_protocol:
Long range contacts were generated using T4 ligase and chromatin immunoprecipitation with H3K27ac antibody (Active motif, 39133) was performed for protein enrichment.
Library was generated using Tn5 transposition and Nextera adapters.

value: Neuronal progenitor cell

tag: chip antibody

value: Active Motif, 39133

tag: treatment

value: Crosslinked with 1% formaldehyde


title: CTL rep2


title: S1_GEX

description: Library name: OX07_GEX

value: Aqueous humour

tag: type of_uveitis

value: Toxoplasmosis posterior uveitis

value: Infectious

value: R

value: F


title: ALL survivor 100


title: F33 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F33_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: neuronal progenitor cells


title: ALL survivor 93

value: Whole blood


title: S8_GEX

description: Library name: OX19_GEX

value: Undifferentiated acute anterior uveitis

value: NEG

tag: infectious or_non-infectious

value: L

value: Afro-Caribbean


title: IP for GFP PCBP1, 21H7 treatment, rep3

city: Chapel Hill

first: Maria

last: Aleman

state: NC

address: 120 Mason Farm Rd.

institute: University of North Carolina at Chapel Hill

description: Library name: PCBP1_GFP_21H7_C_IP

library_source: other

data_processing:
Salmon (v1.10.2)  was used for transcript abundance quantification which was then analyzed for differential bound RNAs using DESeq2 (v3.19)  with a Likelihood Ratio test where bound RNAs were controlled for baseline expression by comparison to input samples.
Assembly: hg38
Supplementary files format and content: text files include TPM for each sample

molecule: other

extract_protocol:
RNeasy Kit with DNase I treatment (Qiagen).
Library preparation of isolated RNA from Flag-PCBP1 immunoprecipitations or from whole cell lysates (inputs) was performed with the KAPA RNA Hyperprep Kit with RiboErase using NEBNext Multiplex Oligos compatible with Illumina sequencing.

value: Chelator


title: CTL rep1

value: Thy1.2+ splenocytes

value: MiG-empty


title: IP for GFP PCBP1, 21H7 treatment, rep2

description: Library name: PCBP1_GFP_21H7_B_IP


title: OSM rep3

value: MiG-OSM


title: ALL survivor 92

value: Male


title: ALL survivor 91


title: F21 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F21_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: Female


title: IP for GFP PCBP1, 21H7 treatment, rep1

description: Library name: PCBP1_GFP_21H7_A_IP


title: OSM rep2


title: F20 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F20_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: IP for GFP PCBP1, DMSO treatment, rep3

description: Library name: PCBP1_GFP_DMSO_C_IP

value: Control


title: OSM rep1


title: F19 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F19_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: IP for GFP PCBP1, DMSO treatment, rep2

description: Library name: PCBP1_GFP_DMSO_B_IP


title: F30 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F30_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: T_JAK2_OSM_KO rep3

value: Jak2V617F Osm-/-


title: F28 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F28_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 88


title: T_JAK2_OSM_KO rep2


title: F17 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F17_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: IP for GFP PCBP1, DMSO treatment, rep1

description: Library name: PCBP1_GFP_DMSO_A_IP


title: ALL survivor 87


title: IP for ∆Fe PCBP1, 21H7 treatment, rep3

description: Library name: PCBP1_Fe_21H7_C_IP


title: F22 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F22_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: F16 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F16_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 86


title: T_JAK2_OSM_KO rep1


title: IP for ∆Fe PCBP1, 21H7 treatment, rep2

description: Library name: PCBP1_Fe_21H7_B_IP


title: T_JAK2_OSM_WT rep3

value: Jak2V617F Osm+/+


title: T_JAK2_OSM_WT rep2


title: ALL survivor 84


title: ALL survivor 90


title: IP for ∆Fe PCBP1, 21H7 treatment, rep1

description: Library name: PCBP1_Fe_21H7_A_IP


title: F14 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F14_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 85


title: F15 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F15_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 89


title: T_JAK2_OSM_WT rep1


title: F13 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F13_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: IP for ∆Fe PCBP1, DMSO treatment, rep2

description: Library name: PCBP1_Fe_DMSO_B_IP


title: ALL survivor 83


title: AdhEarly.rep2

city: Singapore

first: Zhengwei

last: Wu

address: 60 Biopolis St

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Reads were mapped to Homo sapiens genome assembly GRCh37/hg19 using STAR alignment software and read counts obtained with RSEM.
Data was filtered to exclude lowly-expressed genes (count per million > 1 in 25% or more samples). Next, data was filtered for known protein-coding genes and normalized using TMM.
Next, data was adjusted for heteroskedasticity using limma package (R version 4.2).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include log2 normalized values for each Sample

source_name: Adh

growth_protocol: TS cell line was maintained using Dulbecco’s Modified Eagle Medium F-12 (DMEM F-12) media supplemented with 10% Bovine Serum Albumin (BSA). Adh cell line was maintained using Dulbecco’s Modified Eagle Medium F-12 (DMEM F-12) media supplemented with 10% (v/v) Fetal Bovine Serum (FBS).

extract_protocol: Cells were first harvested by trypsinization and cell pellet was subjected to RNA extraction according to the protocol provided in AllPrep DNA/RNA mini kit (Qiagen). RNA was then quantified using NanoDrop™ 2000 Spectrophotometer. RNA samples were prepared for library preparation at 2.0ug per sample.

treatment_protocol: TS and Adh cell lines were subjected to glucose limitation for 48 hours.

value: Adh

value: Early


title: F18 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F18_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: neuronal progenitor cells


title: IP for ∆Fe PCBP1, DMSO treatment, rep1

description: Library name: PCBP1_Fe_DMSO_A_IP


title: F12 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F12_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 82

source_name: Whole blood

value: Whole blood


title: F10 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F10_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 81


title: IP for ∆RNA PCBP1, 21H7 treatment, rep3

description: Library name: PCBP1_RNA_21H7_C_IP


title: AdhEarly.rep1


title: ALL survivor 80


title: F07 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F07_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: Adh_ULG_rep2

value: ULG


title: IP for ∆RNA PCBP1, 21H7 treatment, rep2

description: Library name: PCBP1_RNA_21H7_B_IP


title: Adh_ULG_rep1


title: IP for ∆Fe PCBP1, DMSO treatment, rep3

description: Library name: PCBP1_Fe_DMSO_C_IP


title: IP for ∆RNA PCBP1, 21H7 treatment, rep1

description: Library name: PCBP1_RNA_21H7_A_IP


title: ALL survivor 79


title: ALL survivor 78


title: Adh_HG_rep1

value: HG


title: IP for ∆RNA PCBP1, DMSO treatment, rep2

description: Library name: PCBP1_RNA_DMSO_B_IP


title: F05 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F05_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: IP for ∆RNA PCBP1, DMSO treatment, rep3

description: Library name: PCBP1_RNA_DMSO_C_IP


title: Adh_HG_rep2


title: F04 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F04_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: TS.UL.rep2

source_name: TS

value: TS

value: UL


title: ALL survivor 77


title: F03 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F03_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: IP for ∆RNA PCBP1, DMSO treatment, rep1

description: Library name: PCBP1_RNA_DMSO_A_IP


title: TS.UL.rep1


title: IP for WT PCBP1, 21H7 treatment, rep3

description: Library name: PCBP1_WT_21H7_C_IP

value: Chelator


title: SP2509h_Rep6

city: Boston

first: Manish

middle: V.

last: Bais

state: MA

address: W216, 700 Albany street

department: Translational Dental Medicine

institute: Boston University

data_processing:
Proprietary perl script developed by NOVOGENE bioinformatics facility.
Reference genome alignment using HISAT2.
Gene expression quantification using featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized count for each samples

source_name: Tongue

extract_protocol:
RNA was isolated using TRIzol and purified with RNeasy Mini kit (Qiagen). Around 400 nanogram of RNA was used for sequencing at NOVOGENE facility.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.

value: Tongue


title: ALL survivor 76


title: ALL survivor 75


title: TS.WT.rep2

value: WT


title: ALL survivor 74


title: ALL survivor 73


title: IP for WT PCBP1, 21H7 treatment, rep2

description: Library name: PCBP1_WT_21H7_B_IP


title: SP2509h_Rep5


title: F06 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: F06_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: TS.WT.rep1


title: IP for WT PCBP1, 21H7 treatment, rep1

description: Library name: PCBP1_WT_21H7_A_IP


title: SP2509h_Rep4


title: ALL survivor 72


title: SP2509h_Rep3


title: IP for WT PCBP1, DMSO treatment, rep3

description: Library name: PCBP1_WT_DMSO_C_IP


title: 7d_S46_L007_Male_Brain_Probiotic

city: Columbia

first: Trupti

last: Joshi

state: Missouri

address: 103 Math Science Building

department: Department of Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME)

institute: University of Missouri-Columbia

description: Library name: 7d_S46_L007

data_processing:
The trimmed sequence reads ere mapped to GRCm39 using Hisat2
fpkm files are estimted using cufflinks
Assembly: mm39
Supplementary files format and content: gene_fpkm

source_name: Brain

extract_protocol:
Total RNA was extracted by using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (Cat. No. 80224; Qiagen, MD, USA) in accordance with the manufacturer’s protocol.
Libraries were constructed following the manufacturer’s protocol with reagents supplied in the Illumina mRNA Stranded Library Preparation Kit and sequenced at the University of Missouri Genomics Technology Core.

treatment_protocol: Eight adult (~8-12 week old) wild type mouse dams were randomly assigned to receive one capsule of a probiotic supplement (Bio-Kult Everyday Probiotic  Supplement, BIOKULT LIMITED, Manchester, United Kingdom) that was dispensed in 100mL of water and was changed triweekly or water alone (Controls) for two weeks before pairing for breeding and continued to receive the probiotic throughout pairing and pregnancy.

value: Brain

value: Probiotic


title: 7b_S30_L007_Male_Placenta_Probiotic

description: Library name: 7b_S30_L007

source_name: Placenta

value: Placenta

value: Male


title: SP2509h_Rep1


title: ALL survivor 71


title: ALL survivor 70

value: Female


title: 6d_S45_L007_Female_Brain_Probiotic

description: Library name: 6d_S45_L007


title: IP for WT PCBP1, DMSO treatment, rep2

description: Library name: PCBP1_WT_DMSO_B_IP

value: Control


title: 6b_S29_L007_Female_Brain_Probiotic

description: Library name: 6b_S29_L007


title: IP for WT PCBP1, DMSO treatment, rep1

description: Library name: PCBP1_WT_DMSO_A_IP


title: Vehicle_Rep3

value: Vehicle


title: Input for GFP PCBP1, 21H7 treatment, rep2

description: Library name: PCBP1_GFP_21H7_B_input


title: ALL survivor 68


title: 60b_S44_L007_Female_Placenta_Control

description: Library name: 60b_S44_L007


title: Vehicle_Rep2


title: Input for GFP PCBP1, 21H7 treatment, rep1

description: Library name: PCBP1_GFP_21H7_A_input


title: ALL survivor 67


title: Vehicle_Rep4


title: 59b_S43_L007_Male_Placenta_Control

description: Library name: 59b_S43_L007


title: Vehicle_Rep1


title: Input for GFP PCBP1, DMSO treatment, rep3

description: Library name: PCBP1_GFP_DMSO_C_input


title: ALL survivor 65


title: 52d_S57_L008_Male_Brain_Probiotic

description: Library name: 52d_S57_L008


title: Input for GFP PCBP1, DMSO treatment, rep2

description: Library name: PCBP1_GFP_DMSO_B_input


title: Left Experimental 3

city: Cambridge

first: Alberto

last: Rosello-Diez

address: Physiology building. Downing St.

department: Physiology, Development and Neuroscience

institute: University of Cambridge

data_processing:
Following sequencing, fastq reads were mapped against a custom reference that combined Mus musculus (GRCm38) with transgenic genes (tdTomato, ECFP, and WPRE) using CellRanger (v6.0.2). The resulting aligned reads were analysed via R (4.0.2). Seurat (v.4.2.1) and R/Bioconductor SingleCellExperiment packages were used to generate count matrices. For each sample, the mean of unique molecular identifiers (UMIs) (nCounts) was calculated and used as a threshold to exclude empty droplets. Filtering was manually done according to the nCount and number of genes. DoubletFinder (v2.0.3) was used to remove the expected doublets in each sample. Harmony R package (v0.1.0) was also used to mitigate remove batch effects, and subsequently the data were consolidated into a single Seurat object.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Knee (Whole tissue)

extract_protocol:
The knee region (obtained via orthogonal cuts from the hypertrophic region of the distal femur to the hypertrophic region of the proximal tibia in skinned hindlimbs) of E16.5 Left and Right limbs from Ctl and Left-Cart-p21 samples (2 embryos of each genotype) were collected in DMEM with 10% DMSO and 5% calf serum, stored in a MrFrosty (ThermoFisher) at 4ºC for 10 min and then transferred to -80ºC overnight. Tissue lysis and nuclei isolation were done as described by L.G.M. in https://www.protocols.io/view/frankenstein-protocol-for-nuclei-isolation-from-f-5jyl8nx98l2w/v2, in two batches of four samples each (left and right knees from one control and one experimental embryo).
The libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics) according to manufacturer’s directions. The libraries were sequenced twice on Novaseq (~800 million clusters/read pairs each time, which when combined amounted to ~40,000 reads per nuclei across the 8 samples).

value: Knee (Whole tissue)

value: Chondrocytes+ surrounding  tissue

value: Pitx2-Cre/+;  Col2a1-eCFP/+; TigreDragon-p21/+


title: ALL survivor 64

value: Whole blood


title: ALL survivor 69


title: Input for GFP PCBP1, DMSO treatment, rep1

description: Library name: PCBP1_GFP_DMSO_A_input


title: 52b_S42_L007_Male_Placenta_Probiotic

description: Library name: 52b_S42_L007


title: Input for ∆Fe PCBP1, 21H7 treatment, rep3

description: Library name: PCBP1_Fe_21H7_C_input


title: Input for GFP PCBP1, 21H7 treatment, rep3

description: Library name: PCBP1_GFP_21H7_C_input


title: Right Experimental 2


title: 64d_S59_L008_Male_Brain_Control

description: Library name: 64d_S59_L008


title: SP2509h_Rep2


title: ALL survivor 62


title: Right Control 2


title: Right Experimental 3


title: ALL survivor 66


title: 58d_S58_L008_Female_Brain_Control

description: Library name: 58d_S58_L008


title: ALL survivor 61


title: Input for ∆Fe PCBP1, 21H7 treatment, rep1

description: Library name: PCBP1_Fe_21H7_A_input


title: 50b_S41_L007_Male_Placenta_Probiotic

description: Library name: 50b_S41_L007


title: Input for ∆Fe PCBP1, DMSO treatment, rep3

description: Library name: PCBP1_Fe_DMSO_C_input


title: ALL survivor 60


title: 50d_S56_L008_Male_Brain_Probiotic

description: Library name: 50d_S56_L008


title: 42b_S40_L007_Male_Placenta_Probiotic

description: Library name: 42b_S40_L007


title: Right Control 1


title: Left Control 2


title: Input for ∆Fe PCBP1, 21H7 treatment, rep2

description: Library name: PCBP1_Fe_21H7_B_input


title: ALL survivor 59


title: ALL survivor 63


title: Input for ∆Fe PCBP1, DMSO treatment, rep2

description: Library name: PCBP1_Fe_DMSO_B_input


title: Left Experimental 2


title: 41d_S54_L008_Female_Brain_Probiotic

description: Library name: 41d_S54_L008


title: Input for ∆Fe PCBP1, DMSO treatment, rep1

description: Library name: PCBP1_Fe_DMSO_A_input


title: Left Control 1


title: ALL survivor 57


title: Hindlimb, tdt_negative EXP+CTL 2, Collection 2

description: 25 min digestion with Acuumax, followed by Collagenease B (5mg/ml) treatment for  ~90min at 37 C.

data_processing:
The fastq files were aligned against a custom reference comprising Mus musculus (GRCm38; obtained from 10X Genomics Ref.) along with transgenic genes (tdTom, CreERT2, and WPRE) using CellRanger (v7.2.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hindlimb

extract_protocol:
At E14.5, the hindlimb samples (femur and tibia) were carefully dissected. Following, the tissue underwent treatment with Accumax in a rocker at 31°C for 25 minutes and they were gently shaken every 10 min. The supernatant was carefully transferred into a tube and placed on ice for preservation, while the cartilaginous portions were exposed to Collagenase B (5 mg/ml; Sigma) for ~90 min at 37°C in a water bath (and pipetted every 20 min). To stop collagenase activity, we then added 700 µl of cold DMEM+20% FBS for each tube. We then incorporated outer and inner supernatants, and the samples were resuspended in 20 volumes of 1× RBC lysis buffer and incubated for 10 minutes at room temperature on a rocker.  As a final step, the cell suspension was filtered through 40-μm Flowmi® Cell Strainers and cells were stained with DAPI (stock concentration: 0.05 µg/ml) and transferred into Falcon™ Round-Bottom Polypropylene (Fisher Scientific). The tdT+ and tdT- cells were sorted using flow cytometry  and the samples were then multiplexed based on sex and conditions.
The libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics) according to manufacturer’s directions and then sequenced on Illumina (~ 833 million clusters/read pairs each time) with a length of 100 bp.

value: Hindlimb

value: 25 min Accumax and Collagenease B (90 min)


title: Input for ∆RNA PCBP1, 21H7 treatment, rep3

description: Library name: PCBP1_RNA_21H7_C_input


title: 37d_S53_L008_Male_Brain_Probiotic

description: Library name: 37d_S53_L008


title: Hindlimb, tdt_positive EXP+CTL 2, Collection 2


title: Input for ∆RNA PCBP1, 21H7 treatment, rep2

description: Library name: PCBP1_RNA_21H7_B_input


title: ALL survivor 56


title: 37b_S38_L007_Male_Placenta_Probiotic

description: Library name: 37b_S38_L007


title: Hindlimb, tdt_negative EXP+CTL 1, Collection 1


title: Input for ∆RNA PCBP1, 21H7 treatment, rep1

description: Library name: PCBP1_RNA_21H7_A_input


title: ALL survivor 55


title: 34b_S37_L007_Female_Placenta_Probiotic

description: Library name: 34b_S37_L007


title: Hindlimb, tdt_positive EXP+CTL 1, Collection 1


title: Input for ∆RNA PCBP1, DMSO treatment, rep3

description: Library name: PCBP1_RNA_DMSO_C_input


title: ALL survivor 53


title: Right gonad, female, E5

city: University Park

first: Tae Hyun

last: Kim

state: PA

address: 317 AVBS

institute: Penn State University

description: single-cell RNAseq

data_processing:
Cell Ranger (6.1.1) and the expression matrices were generated using the "count" command and used for subsequent analysis using the Seurat V4 R package.
Assembly: GRCg6a NCBI Gallus gallus Annotation Release 104
Supplementary files format and content: filtered_feature_bc_matrix.h5 file output from Cell Ranger

organism: Gallus gallus

source_name: Gonad

extract_protocol:
E5 female gonads were separately collected from each side and dissociated using trypsin-EDTA, followed by filtration through a 40 μm cell strainer. A dead-cell removal kit was then used to improve cell viability.
10× Chromium Next GEM Single Cell 3′ v3.1 protocol (10× Genomics)

value: Gonad

value: female

value: gonadal cells

value: Leghorn

tag: developmental stage


title: Input for ∆RNA PCBP1, DMSO treatment, rep2

description: Library name: PCBP1_RNA_DMSO_B_input


title: 30d_S52_L008_Male_Brain_Control

description: Library name: 30d_S52_L008

value: Brain


title: ALL survivor 52

data_processing:
The raw IDAT files were processed into β-values, which quantify DNA methylation levels on a scale from 0 to 1, using the minfi package from Bioconductor in R v4.1.1. The data was then normalized using the preprocessIllumina function in minfi to correct for technical variation. The preprocessing pipeline included several filtering steps: removal of non-specific probes; exclusion of probes with detection p-values greater than 0.05 in more than 25% of samples; elimination of probes located near SNPs (within 10 bp of the CpG site or single base extension) or associated with SNPs having a minor allele frequency above 1%; removal of probes with β-values of 0 or 1 in more than 0.25% of samples; exclusion of non-CpG probes; and filtering out probes located on sex chromosomes. Quality control was performed using standard minfi metrics such as median intensity plots, density distributions, and control probe assessments, with all samples passing QC and included in the final analysis.
normalized betas


title: ALL survivor 58


title: ALL survivor 54


title: 30b_S36_L007_Male_Placenta_Control

description: Library name: 30b_S36_L007


title: 29d_S51_L008_Female_Brain_Control

description: Library name: 29d_S51_L008


title: 41b_S39_L007_Female_Placenta_Probiotic

description: Library name: 41b_S39_L007

value: Probiotic


title: PK-15 cells，pH108R overexpression，TNFα-3

city: Zhengzhou

first: Enping

last: Liu

address: 100 Kexue Avenue

country: China

institute: Zhengzhou university

description: Library name: P-TNF3

data_processing:
The reference genome sequence for mapping was NCBI_Sscrofa11.1
Assembly: NCBI_Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: kidney

growth_protocol: PK-15 cells were cultured  in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) containing 10% (v/v) fetal bovine serum and 1% streptomycin and penicillin.

extract_protocol:
Total RNA was isolated from cells with TRIZOL reagent (Invitrogen), 2ug total RNA were used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq library prep kit following manufacturer's protocols.

value: kidney

value: Epithelial cells

value: WT

value: TNFα


title: PK-15 cells，pH108R overexpression，TNFα-2

description: Library name: P-TNF2


title: Input for WT PCBP1, 21H7 treatment, rep2

description: Library name: PCBP1_WT_21H7_B_input

value: Chelator


title: 29b_S35_L007_Female_Placenta_Control

description: Library name: 29b_S35_L007

value: Placenta

value: Female

value: Control


title: Input for WT PCBP1, 21H7 treatment, rep3

description: Library name: PCBP1_WT_21H7_C_input


title: ALL survivor 50

extract_protocol: Genomic DNA was extracted from blood samples using DNEasy (Qiagen) chemistry and columns. No modification was made to the manufacturer's specifications.

value: Whole blood


title: Input for ∆RNA PCBP1, DMSO treatment, rep1

description: Library name: PCBP1_RNA_DMSO_A_input


title: Left gonad, female, E5

description: single-cell RNAseq


title: ALL survivor 51


title: 20d_S50_L008_Male_Brain_Control

description: Library name: 20d_S50_L008

value: Male


title: PK-15 cells，pH108R overexpression，TNFα-1

description: Library name: P-TNF1


title: ALL survivor 49


title: Input for WT PCBP1, 21H7 treatment, rep1

description: Library name: PCBP1_WT_21H7_A_input


title: PK-15 cells，pH108R overexpression，mock-3

description: Library name: P-mock3

value: PBS


title: Input for WT PCBP1, DMSO treatment, rep3

description: Library name: PCBP1_WT_DMSO_C_input


title: 20b_S34_L007_Male_Placenta_Control

description: Library name: 20b_S34_L007


title: 19d_S49_L008_Female_Brain_Control

description: Library name: 19d_S49_L008


title: ALL survivor 48


title: ALL survivor 47


title: PK-15 cells，pH108R overexpression，mock-2

description: Library name: P-mock2


title: 19b_S33_L007_Female_Placenta_Control

description: Library name: 19b_S33_L007


title: PK-15 cells，pH108R overexpression，mock-1

description: Library name: P-mock1


title: Input for WT PCBP1, DMSO treatment, rep2

description: Library name: PCBP1_WT_DMSO_B_input


title: ALL survivor 46


title: 13d_S48_L007_Female_Brain_Control

description: Library name: 13d_S48_L007


title: ALL survivor 45


title: 13b_S32_L007_Female_Placenta_Control

description: Library name: 13b_S32_L007


title: Input for WT PCBP1, DMSO treatment, rep1

description: Library name: PCBP1_WT_DMSO_A_input


title: PK-15 cells，TNFα-3

description: Library name: V-TNF3


title: ALL survivor 44


title: 12d_S47_L008_Male_Brain_Control

description: Library name: 12d_S47_L007


title: ALL survivor 43


title: PK-15 cells，TNFα-1

description: Library name: V-TNF1


title: 12b_S31_L007_Male_Placenta_Control

description: Library name: 12b_S31_L007


title: HUVEC TIE2-WT, rep 2

city: Cincinnati

first: Sandra

last: Schrenk

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

description: Library name: EB10

data_processing:
The RNA-seq data were analyzed using the nf-core RNA-seq pipeline (v3.18.0). The pipeline was executed with default parameters unless specified otherwise, using mm10 as the reference genome.
Raw sequencing reads were assessed for quality using FastQC (v0.12.1).
Adapter sequences and low-quality reads were removed using Trim Galore (v0.6.10). Filtered reads were aligned to the reference genome using STAR (v2.6.1d).
Transcript quantification was performed using Salmon (v1.10.3) in alignment-based mode.
Post-alignment metrics, including duplication rates and coverage statistics, were generated using Qualimap (v2.3) and RSeQC (v5.0.2).
Assembly: hg38
Supplementary files format and content: Matrix table (tab-delimited text file) including tpm values for all genes in all samples

source_name: Umbilical cord

growth_protocol: Cells were grown in Endothelial Growth Medium in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was isolated using RNAeasy mini kit (Quiagen). 500ng was used as an input for library preparation.
NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs) was used for unique dual index library preparation under PCR cycle number of 9.

value: Umbilical cord

value: human umbilical vein endothelial cell (HUVEC)


title: PK-15 cells，control-3

description: Library name: V-mock3


title: ALL survivor 42


title: HUVEC TIE2-WT, rep 3

description: Library name: EB11


title: WT, IR, Input, rep 4, MeRIP-seq

city: Chicago

first: Dapeng

last: Chen

state: Illinois

address: 900 E 57th St

institute: UChicago

description: Library name: WT_IR_m6Aseq_Input_rep4

data_processing:
Fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads
STAR software (v2.7.9a) was used to align the high-quality clean reads to the mouse reference genome (mm39)
featureCounts software (v2.0) was used to get the raw gene level mRNA read counts as the mRNA expression profile
MACS2 (version 2.2.7.1) was used for peak calling.
Assembly: mm39
Supplementary files format and content: CSV file including read counts for each sample in RNA seq
Supplementary files format and content: CSV files including peaks for each sample in RIP seq and m6A seq
Library strategy: MeRIP-Seq

source_name: Tumor

growth_protocol: Tumor-infiltrating DCs were collected on day 5 post irradiation

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit. YTHDF2 antibody (aviva systems) was used for  extraction of YTHDF2-binding RNA. m6A antibody (NEB Epimark) was used for extraction of m6A modified RNA
Library was constructed using Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

treatment_protocol: Tumors were irradiated with 20 Gy of irradiation

value: Tumor

value: Dendritic cells

value: Immune cells

value: IR


title: HUVEC TIE2-WT, rep 1

description: Library name: EB9


title: ALL survivor 41


title: HUVEC TIE2-WT, rep 4

description: Library name: EB12


title: WT, IR, Input, rep 3, MeRIP-seq

description: Library name: WT_IR_m6Aseq_Input_rep3


title: PK-15 cells，control-2

description: Library name: V-mock2

value: kidney


title: PK-15 cells，control-1

description: Library name: V-mock1

value: Epithelial cells


title: ALL survivor 40


title: HUVEC TIE2-L914F, rep 3

description: Library name: EB7


title: HUVEC TIE2-L914F, rep 2

description: Library name: EB6


title: WT, IR, Input, rep 1, MeRIP-seq

description: Library name: WT_IR_m6Aseq_Input_rep1

value: WT


title: ALL survivor 39


title: RR-E17-5: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 17 embryonic age

city: Beijing

first: Qiang

last: Huang

address: No. 2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

description: Library name: Unknown_AU543-01T0077

data_processing:
In the preprocessing stage, Cutadapt (version 4.4)  was used to eliminate adapter sequences and low-quality reads for all samples. The clean data were subsequently aligned to the chicken reference genome (GRCg7b) using HISAT 2 (version 2.2.1)  with default parameters. Based on the alignment data, transcripts were assembled and quantified using StringTie. To generate the gene count matrix, we utilized the prepDE.py Python script, which is distributed as part of the StringTie, to process the output files generated by StringTie. The gene expression data for each group was filtered in R program to retain only protein-coding genes.
Assembly: GRCg7b
Supplementary files format and content: All_samples_read_counts.csv files include read counts for each Sample
Supplementary files format and content: D42/D21/D1/E17_DEGs.csv include differentially expressed genes for each growth points

source_name: breast muscle myofibroblasts

extract_protocol:
Approximately 20 mg of frozen breast muscle tissue per sample was homogenized in the lysis buffer provided in the RNA extraction kit (LS1040, Promega, Shanghai, China) following the manufacturer’s instructions. Total RNA was then extracted according to the kit protocol. The quality of the isolated RNA was assessed by detecting degradation and potential contamination using 1% agarose gels.
The cDNA libraries were constructed using Illumina Truseq TM RNA Sample Prep Kit (Illumina, USA) according to the manufacturer's guide.

value: breast muscle myofibroblasts

value: male broiler

tag: time

value: 17 embryonic years


title: WT, IR, Input, rep 2, MeRIP-seq

description: Library name: WT_IR_m6Aseq_Input_rep2


title: PK-15 cells，TNFα-2

description: Library name: V-TNF2

value: TNFα


title: RR-E17-6: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0078


title: ALL survivor 38


title: ALL survivor 37


title: HUVEC NT, rep 4

description: Library name: EB4

value: NT


title: WT, IR, m6A IP, rep 3, MeRIP-seq

description: Library name: WT_IR_m6Aseq_IP_rep3


title: RR-E17-3: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0075


title: HUVEC NT, rep 3

description: Library name: EB3


title: HUVEC TIE2-L914F, rep 4

description: Library name: EB8


title: RR-E17-2: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0074


title: ALL survivor 36

value: Whole blood

value: Female


title: ALL survivor 35


title: HUVEC NT, rep 2

description: Library name: EB2


title: WT, IR, m6A IP, rep 1, MeRIP-seq

description: Library name: WT_IR_m6Aseq_IP_rep1


title: HUVEC TIE2-L914F, rep 1

description: Library name: EB5


title: ALL survivor 34

value: Male


title: RR-E17-1: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0073


title: WT, Control, Input, rep 4, MeRIP-seq

description: Library name: WT_Control_m6Aseq_Input_rep4

value: Control


title: CR-E17-6: Crossbred progeny, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0072


title: ALL survivor 33


title: RR-E17-4: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0076


title: 6b, scRNAseq

first: Pengda

middle: P.

last: Lie

address: 21-246 Lineberger Cancer Center

department: Biochemistry and Biophysics

description: 10x Genomics

data_processing:
Resulting datasets were analyzed via the Seurat package (v5.1.0) in R (v4.3.1). Raw counts were processed following standard quality control measures and low-quality cells were excluded, including dead and suspected doublets. The minimum number of principal components needed to represent the data were calculated using a Jack Straw Plot, and next clustering was performed at a resolution of 0.7
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: B16 tumors

extract_protocol:
On day 14, tumor tissues were digested using the tumor dissociation kit, mouse and gentleMACS Dissociator. Tumor debris and melanin were removed by filtration and PBS washing. Tumor-infiltrating CD45+ cells in B16 tumors were enriched through positive selection via anti-CD45 biotinylated antibody staining for 20 min at room temperature, streptavidin-labeled microbeads and Miltenyi MACS LS columns. CD45+ cells from three mice in each treatment group were pooled together in PBS and sent for sample preparation.
PE-CD45+/Annexin V- cells were sorted on a SONY XYZ instrument, and 10000 cells were loaded in 10x Genomics Chromium Single Cell 3’ inlets (one inlet per sample). Barcoding and library preparation were performed following manufacture instructions with the 10x Genomics Chromium GEM-X Single Cell 3’ kit v4

treatment_protocol: B16 tumor-beraring C57BL/6J mice were treated with or without 60 mg/kg of SPOP-IN-6b for 9 consecutive days starting from 5 days after subcutaneous inoculation of B16 cells.

value: B16 tumors

tag: strain

tag: age

value: CD45+ lymphocytes

value: 60 mg/kg of 6b


title: WT, IR, m6A IP, rep 4, MeRIP-seq

description: Library name: WT_IR_m6Aseq_IP_rep4

tag: tissue

value: Tumor

value: Dendritic cells

value: Immune cells


title: ALL survivor 32

first: Daniel

last: Sinnett

address: 3175 Chem. de la Côte-Sainte-Catherine

tag: Sex


title: WT, Control, Input, rep 2, MeRIP-seq

description: Library name: WT_Control_m6Aseq_Input_rep2

tag: cell type


title: CR-E17-4: Crossbred progeny, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0070


title: CR-E17-5: Crossbred progeny, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0071


title: ALL survivor 31


title: WT, Control, Input, rep 1, MeRIP-seq

description: Library name: WT_Control_m6Aseq_Input_rep1


title: CR-E17-3: Crossbred progeny, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0069


title: ALL survivor 30


title: C1QBP-NC-2

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

description: Library name: Sample 5 RNA-seq

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Bile duct

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Bile duct

value: wt

value: siNC


title: CR-E17-2: Crossbred progeny, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0068

value: breast muscle myofibroblasts

value: male broiler


title: ALL survivor 29

city: Montréal

institute: CHU Sainte-Justine


title: C1QBP-NC-1

description: Library name: Sample 4 RNA-seq


title: C1QBP-NC-3

description: Library name: Sample 6 RNA-seq


title: WT, Control, m6A IP, rep 3, MeRIP-seq

description: Library name: WT_Control_m6Aseq_IP_rep3

value: WT


title: HUVEC NT, rep 1

description: Library name: EB1

value: Umbilical cord

value: human umbilical vein endothelial cell (HUVEC)

value: NT


title: WT, Control, m6A IP, rep 4, MeRIP-seq

description: Library name: WT_Control_m6Aseq_IP_rep4


title: C1QBP-Si-3

description: Library name: Sample 3 RNA-seq


title: CR-E17-1: Crossbred progeny, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0067

value: 17 embryonic years


title: ALL survivor 28

value: Whole blood

value: Male


title: WT, Control, Input, rep 3, MeRIP-seq

description: Library name: WT_Control_m6Aseq_Input_rep3

value: Control


title: CC-E17-6: Cornish purebred, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0066


title: WT, Control, m6A IP, rep 2, MeRIP-seq

description: Library name: WT_Control_m6Aseq_IP_rep2


title: WT, IR, m6A IP, rep 2, MeRIP-seq

description: Library name: WT_IR_m6Aseq_IP_rep2

value: IR


title: ALL survivor 26

value: Female


title: WT, Control, m6A IP, rep 1, MeRIP-seq

description: Library name: WT_Control_m6Aseq_IP_rep1

value: Tumor

value: Dendritic cells


title: CC-E17-5: Cornish purebred, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0065


title: WT, IR, Input, rep 5, RIP-seq

description: Library name: WT_IR_RIPseq_Input_rep5

data_processing:
Fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads
STAR software (v2.7.9a) was used to align the high-quality clean reads to the mouse reference genome (mm39)
featureCounts software (v2.0) was used to get the raw gene level mRNA read counts as the mRNA expression profile
MACS2 (version 2.2.7.1) was used for peak calling.
Assembly: mm39
Supplementary files format and content: CSV file including read counts for each sample in RNA seq
Supplementary files format and content: CSV files including peaks for each sample in RIP seq and m6A seq

value: Immune cells


title: C1QBP-Si-1

description: Library name: Sample 1 RNA-seq

value: Bile duct


title: HeLa, Meta, macroH2A1, Rep2 (Chip)

city: Minhang

first: deng

last: yongzhuo

state: Shanghai

address: DongchuanoRoad N0.800

institute: Shanghai Jiao Tong University

description: Library name: HeLa_Meta_macroH2A1_Chip, Rep2

data_processing:
Utilize TrimGalore to remove sequencing adapter sequences and low-quality bases from your reads (Q<20)
Use Bowtie2 to align the trimmed single reads to human genome
Use Samtools to remove the unknown chromosome segments mapped reads, unmappable reads and multi-mapped reads The mapped reads are converted to bam format, are de-duplicated by Sambamba markdup
mapped reads are used to identidfy macroH2A1 enriched domains  by normR after normalization by the control (input nucleosome DNA). Genome is divided into 2kb bins,regimeR is used for calling peaks,  significant bins identified by Fisher’s test (P < 0.05) are use exportR to output into Bed files and BigWig files
Assembly: Homo_sapiens.GRCh38.114
Supplementary files format and content: BigWig

source_name: cell line

growth_protocol: All cell lines are kept in a humidified incubator at 37°C temperature with a 5% CO2 supply and cultured in DMEM (GIBCO, Carlsbad, CA, USA) with 10% FBS (GIBCO, Carlsbad, CA, USA) and 1% Pen/Strep antibiotin (GIBCO, Carlsbad, CA, USA).

extract_protocol:
In brief, collected cells are lysis in hypotonic buffer. After centrifugation, then resuspend in PA buffer. Cells are homogenized with a Dounce homogenizer for 10min with intermittent pauses. After removing large debris, supernatant is filtered through 10 μm and 5 μm filters. Chromosomes are centrifuged at 1750 × g for 10 min at 4°C and resuspend in MNase buffer.
Sequencing libraries are generated using approximately 1 ng of DNA per sample with the NEBNext® Ultra™ II DNA Library Prep Kit (E7645S, NEB, Ipswich, MA, USA), and sequencing is conducted on the Illumina® NovaSeq 500 platform. Prior to library preparation, the DNA is extracted using phenol-chloroform and ethanol precipitation. To obtain the DNA, either input mono-nucleosomes or ChIP-purified macroH2A1 nucleosomes are treated overnight at 56°C with 1% SDS and 200 μg/mL Proteinase K (Invitrogen, Carlsbad, CA, USA) following a pre-incubation with 100 μg/mL RNase A (Invitrogen, Carlsbad, CA, USA) to eliminate RNA contamination.

treatment_protocol: Culture cells with 100ng/ml colcemid (Sigma-Aldrich, St. Louis, MO, USA) overnight. After the incubation period, collected cells are lysed for purifing mitotic chromosome

value: cell line

value: human cervical carcinoma cell line

value: epithelial cells


title: ALL survivor 25


title: ALL survivor 24


title: CC-E17-3: Cornish purebred, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0063

value: breast muscle myofibroblasts

value: male broiler


title: WT, IR, Input, rep 4, RIP-seq

description: Library name: WT_IR_RIPseq_Input_rep4

value: WT


title: WT, IR, Input, rep 3, RIP-seq

description: Library name: WT_IR_RIPseq_Input_rep3


title: HeLa, Meta, macroH2A1 (input)

description: Library name: HeLa_Meta_macroH2A1_Control, input


title: ALL survivor 23


title: CC-E17-2: Cornish purebred, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0062


title: HeLa, Meta, macroH2A1, Rep1 (Chip)

description: Library name: HeLa_Meta_macroH2A1_Chip, Rep1


title: ALL survivor 22


title: RR-D1-6: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0054

value: 1 days old


title: CC-E17-1: Cornish purebred, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0061

value: 17 embryonic years


title: ALL survivor 27

value: Whole blood


title: WT, IR, YTHDF2 IP, rep 5, RIP-seq

description: Library name: WT_IR_RIPseq_IP_rep5


title: HeLa, G1/S, macroH2A1, Rep1 (Chip)

description: Library name: HeLa_G1/S_macroH2A1_Chip, Rep1


title: WT, IR, Input, rep 2, RIP-seq

description: Library name: WT_IR_RIPseq_Input_rep2


title: C1QBP-Si-2

description: Library name: Sample 2 RNA-seq


title: WT, IR, Input, rep 1, RIP-seq

description: Library name: WT_IR_RIPseq_Input_rep1


title: RR-D1-5: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0053


title: HeLa, G1/S, macroH2A1, Rep2 (Chip)

description: Library name: HeLa_G1/S_macroH2A1_Chip, Rep2


title: RR-D1-4: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0052


title: HeLa, G1/S, macroH2A1 (input)

description: Library name: HeLa_G1/S_macroH2A1_Control, input


title: ARPE-19, Meta, macroH2A1 (input)

description: Library name: ARPE-19_Meta_macroH2A1_Control, input

value: human retinal pigment epithelial cell line


title: ALL survivor 19

value: Male


title: ALL survivor 21


title: CC-E17-4: Cornish purebred, Transcriptome sequencing of breast muscles, 17 embryonic age

description: Library name: Unknown_AU543-01T0064


title: 42d_S55_L008_Male_Brain_Probiotic

description: Library name: 42d_S55_L008

value: Brain

value: Probiotic


title: WT, IR, YTHDF2 IP, rep 4, RIP-seq

description: Library name: WT_IR_RIPseq_IP_rep4

value: Tumor

value: IR


title: RR-D1-3: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0051


title: ALL survivor 17

value: Female


title: ALL survivor 18


title: RR-D1-2: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0050


title: ARPE-19, G1/S, macroH2A1, Rep2 (Chip)

description: Library name: ARPE-19_G1/S_macroH2A1_Chip, Rep2


title: WT, IR, YTHDF2 IP, rep 2, RIP-seq

description: Library name: WT_IR_RIPseq_IP_rep2

value: Dendritic cells

value: Immune cells


title: ARPE-19, G1/S, macroH2A1, Rep1 (Chip)

description: Library name: ARPE-19_G1/S_macroH2A1_Chip, Rep1

value: cell line


title: WT, IR, YTHDF2 IP, rep 1, RIP-seq

description: Library name: WT_IR_RIPseq_IP_rep1


title: RR-D1-1: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0049


title: ALL survivor 20


title: ALL survivor 16


title: ARPE-19, G1/S, macroH2A1 (input)

description: Library name: ARPE-19_G1/S_macroH2A1_Control, input

value: epithelial cells


title: CR-D1-6: Crossbred progeny, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0048

value: breast muscle myofibroblasts


title: WT, Control, Input, rep 4, RIP-seq

description: Library name: WT_Control_RIPseq_Input_rep4

value: Control


title: CR-D1-5: Crossbred progeny, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0047

value: male broiler


title: KMS20 ID2 OE S2

first: Mehmet

middle: Kemal

last: Samur

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: Library name: KMS20-ID2-2

data_processing:
Alignment to hg19 with bwa mem
Picard MarkDuplicates for deduplication
MACS2 for peak calling
Assembly: hg19
Supplementary files format and content: TDF files for IGV
Supplementary files format and content: bw, bigWig files for genome browser

growth_protocol: All myeloma cell lines were cultured in RPMI-1640supplemented with 10% fetal bovine serum, 1% L-glutamine and 1% penicillin/streptomycin.

extract_protocol:
10,000 cells are suspended in a solution containing tris acetate, potassium acetate, magnesium acetate, NP-40, protease inhibitors, and DMF, and then exposed to TN5 for 30 minutes at 37 degrees centigrade.
Extracted DNA is purified using a Zymo-Spin column, and amplified by PCR.

treatment_protocol: Control and ID2-overexpressing (ID2-OE) cells were incubated with 0.25 µg/ml doxycycline for 24 hours to induce ID2 expression.

value: ID2 OE


title: WT, Control, Input, rep 5, RIP-seq

description: Library name: WT_Control_RIPseq_Input_rep5

value: WT


title: ALL survivor 14

value: Whole blood


title: CR-D1-4: Crossbred progeny, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0046

value: 1 days old


title: KMS20 Control 2

description: Library name: KMS20-CNT2


title: ALL survivor 13


title: WT, Control, Input, rep 3, RIP-seq

description: Library name: WT_Control_RIPseq_Input_rep3


title: CR-D1-3: Crossbred progeny, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0045


title: WT, IR, YTHDF2 IP, rep 3, RIP-seq

description: Library name: WT_IR_RIPseq_IP_rep3


title: ALL survivor 12

value: Male


title: KMS20 Control 1

description: Library name: KMS20-CNT1


title: ALL survivor 11


title: CR-D1-1: Crossbred progeny, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0043


title: WT, Control, YTHDF2 IP, rep 5, RIP-seq

description: Library name: WT_Control_RIPseq_IP_rep5


title: CMV_2b_1_input

city: Shenzhen

first: yujing

last: lin

address: No. 1088 Xueyuan Avenue, Nanshan District, Shenzhen City, Guangdong Province

institute: Southern University of Science and Technology

data_processing:
Adapters and low-quality bases reads were trimmed by Cutadapt software (v1.18).After trimming, reads containing ambiguous nucleotides or with a length <15 nucleotides were filtered out by Trimmomatic (version 0.30).
The clean reads were mapped to the reference genome (TAIR10) with Burrows Wheeler Aligner3 (BWA; version 0.30). Mapping quality (MAPQ) of all aligned reads was concurrently calculated, and only uniquely mapped reads with a MAPQ ≥ 13 were remained for subsequent analysis for each sample4.
Then the mapping reads were used to identify confident m6A peaks with R package exomePeak2.
Differential m6A reads were identified by MeTDiff based on criteria of fold change > 1.5 and FDR <0.05.
Assembly: TAIR10
Supplementary files format and content: txt files that represent gene expression

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Wild type Arabidopsis Col-0 plants were grown in a condition-controlled greenhouse (8 h:16 h, 22 ℃:22 ℃, light:dark cycle).

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent, and Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module. The cleaved RNA fragments were used for IP with m6A-specific antibody, and the resulting IP product was used for library construction.
Libraries were prepared according to Illumina's Protocol. Briefly, DNA was end-repaired using a combination of E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR. The average insert size for the final cDNA library was 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.

treatment_protocol: Arabidopsis plants at 3-week-old were inoculated by wild-type cucumber mosaic virus (CMV) and the mutated virus deficient in 2b protein (CMVΔ2b) for 14 days.

value: Leaf

tag: ecotype


title: ALL survivor 10


title: CMV_2b_2_input


title: ALL survivor 15


title: CC-D1-6: Cornish purebred, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0042

tag: cell line


title: CMV_2b_2_IP

data_processing:
*library strategy: meRIP-seq
Adapters and low-quality bases reads were trimmed by Cutadapt software (v1.18).After trimming, reads containing ambiguous nucleotides or with a length <15 nucleotides were filtered out by Trimmomatic (version 0.30).
The clean reads were mapped to the reference genome (TAIR10) with Burrows Wheeler Aligner3 (BWA; version 0.30). Mapping quality (MAPQ) of all aligned reads was concurrently calculated, and only uniquely mapped reads with a MAPQ ≥ 13 were remained for subsequent analysis for each sample4.
Then the mapping reads were used to identify confident m6A peaks with R package exomePeak2.
Differential m6A reads were identified by MeTDiff based on criteria of fold change > 1.5 and FDR <0.05.
Assembly: TAIR10
Supplementary files format and content: txt files that represent gene expression


title: KMS20 ID2 OE S1

description: Library name: KMS20-ID2-1


title: ALL survivor 9


title: WT, Control, YTHDF2 IP, rep 3, RIP-seq

description: Library name: WT_Control_RIPseq_IP_rep3


title: ALL survivor 8


title: CC-D1-5: Cornish purebred, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0041


title: CMV_2b_1_IP


title: CC-D1-4: Cornish purebred, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0040


title: WT, Control, YTHDF2 IP, rep 2, RIP-seq

description: Library name: WT_Control_RIPseq_IP_rep2


title: WT, Control, Input, rep 2, RIP-seq

description: Library name: WT_Control_RIPseq_Input_rep2


title: ALL survivor 7


title: CC-D1-3: Cornish purebred, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0039


title: WT, Control, YTHDF2 IP, rep 1, RIP-seq

description: Library name: WT_Control_RIPseq_IP_rep1


title: ALL survivor 6


title: CMV_1_input

value: CMV


title: WT, Control, Input, rep 1, RIP-seq

description: Library name: WT_Control_RIPseq_Input_rep1

value: Tumor


title: cKO, IR, r3, mRNA-seq

description: Library name: cKO_IR_mRNAseq_rep3

value: cKO

value: IR


title: CR-D1-2: Crossbred progeny, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0044


title: CC-D1-2: Cornish purebred, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0038


title: ALL survivor 5

value: Female


title: cKO, IR, r2, mRNA-seq

description: Library name: cKO_IR_mRNAseq_rep2

value: Dendritic cells

value: Immune cells


title: CMV_2_IP


title: WT, Control, YTHDF2 IP, rep 4, RIP-seq

description: Library name: WT_Control_RIPseq_IP_rep4


title: CMV_1_IP


title: cKO, IR, r1, mRNA-seq

description: Library name: cKO_IR_mRNAseq_rep1


title: ALL survivor 4


title: RR-D21-6: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0036

value: 21 days old


title: ALL survivor 2


title: MOCK_2_input

value: MOCK


title: RR-D21-5: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0035

value: breast muscle myofibroblasts


title: ALL survivor 3


title: MOCK_1_input


title: WT, IR, rep 3, mRNA-seq

description: Library name: WT_IR_mRNAseq_rep3


title: WT, IR, rep 2, mRNA-seq

description: Library name: WT_IR_mRNAseq_rep2


title: RR-D21-4: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0034

value: male broiler


title: MOCK_2_IP


title: CMV_2_input


title: MOCK_1_IP


title: RR-D21-3: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0033


title: WT, IR, rep 1, mRNA-seq

description: Library name: WT_IR_mRNAseq_rep1


title: PCBP1/2 shRNA in 21H7, Rep2

description: Library name: CHEL_shPCBP_2

data_processing:
Quality of sequencing fastq files was checked using FastQC and MultiQC. Salmon (v1.10.2) was used for transcript abundance quantification which was then analyzed for differential gene expression using DESeq2 (v3.19).
Significant genes were quantified by passing a read count threshold greater than 10, having an absolute log2 fold change greater than 1 and an adjusted P value less than 0.05. To capture alternative splicing, reads were first mapped to human genome build hg38 from Ensembl{Harrison, 2024 #297} using STAR (v2.7.11b){Dobin, 2013 #298}.
Chi-square tests were used to determine significant differences between observed and expected results. Hypergeometric tests were used to calculate the significance of overlapping datasets, where only co-detected genes or events were used as background.
Spearman's rank correlation test was used in correlation analysis.
Assembly: hg38
Supplementary files format and content: text files include TPM for each sample

growth_protocol: K562 cells were cultured in RPMI 1640 with 10% fetal bovine serum and 1x Anti-Anti and incubated at 37° C with 5% CO2.

extract_protocol:
RNeasy Kit with DNase I treatment (Qiagen).
PolyA selection using KAPA mRNA Hyperprep Kit and NEBNext Multiplex Illumina Adaptors

value: PCBP1 and PCBP2 Knockdown


title: PCBP1/2 shRNA in 21H7, Rep3

description: Library name: CHEL_shPCBP_3


title: ALL survivor 1


title: WT, Control, rep 2, mRNA-seq

description: Library name: WT_Control_mRNAseq_rep2

value: WT

value: Control


title: RR-D21-2: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0032


title: CC-D1-1: Cornish purebred, Transcriptome sequencing of breast muscles, 1 days old

description: Library name: Unknown_AU543-01T0037

value: 1 days old


title: WT, Control, rep 1, mRNA-seq

description: Library name: WT_Control_mRNAseq_rep1


title: WT, Control, rep 3, mRNA-seq

description: Library name: WT_Control_mRNAseq_rep3


title: RR-D21-1: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0031


title: PCBP1/2 shRNA in 21H7, Rep1

description: Library name: CHEL_shPCBP_1