title: AFD camt-1 mutant replicate 4


title: MLL-AF9/iFLT3-ITD ON Replicate 2

status: Public on Jan 13 2021

type: SRA

city: Boston

first: Stefan

last: Bjelosevic

state: MA

address: 450 Brookline Ave

department: Department of Pediatric Oncology

country: USA

institute: Dana-Farber Cancer Institute

library_source: transcriptomic

data_processing:
Sequenced reads were demultiplexed using bcl2fastq (v2.17.1.14)
Basic QC performed on fastq files using FASTQC (v0.11.2)
Sequencing reads were trimmed using cutadapt (v1.5) and aligned to the mm10 reference genome using HISAT 2 (v2.0.4)
Read counting across genomic regions was performed using the Subread (v1.5.0-p3) featureCounts function and differential gene expression analysis was performed in Rstudio (R v3.6.1) using Voom-Limma (v3.42.2)
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated values file of featureCounts counts; Comma separated values file of normalized (voom-limma) counts

molecule: total RNA

organism: Mus musculus

source_name: MLL-AF9/iFLT3-ITD Cell Line

growth_protocol: Cells were cultured in Anne Kelso Modified DMEM supplemented with 20% heat-inactivated foetal bovine serum, 100U/mL penicillin, 100 µg/mL streptomycin and 100 µM L-asparagine at 37 degrees celcius and 10% carbon dioxide

extract_protocol:
Cells were lysed in TriZol reagent and total DNAse-treated RNA isolated using the Zymogen RNA mini-prep kit
RNA libraries were prepared using the Lexogen QuantSeq 3'-mRNA Seq Library Prep kit

treatment_protocol: MLL-AF9/iFLT3-ITD cells were steady-state cultured in 1 µg/mL doxycycline (refreshed every 48 hours) to maintain iFLT3-ITD transgene expression (including for non-iFLT3-ITD depleted controls). For depletion experiments, cells were washed twice with PBS and cultured in doxycycline-free medium to deplete iFLT3-ITD transgene expression for the specified time period

tag: cell line

value: Acute myeloid leukaemia cell line (generated by transducing murine foetal liver cells with constitutively expressed MSCV-Luc2-IRES-MLL-AF9 and inducible TRE-tight-DsRED-IRES-FLT3-ITD retroviral vectors)

tag: treatment

value: Untreated control – inducible iFLT3-ITD expression maintained in 1 µg/mL doxycycline


title: LD08:00_1

city: shanghai

first: shiyu

last: sun

address: No.800 dong chuan road

country: China

institute: Shnaghai jiao tong university

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to rice  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Genome_build: Tigr7
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Oryza sativa Japonica Group

source_name: the mitosis stages I anther sample at 08:00 in long-day condition rep_1

growth_protocol: Rice variety Oryza sativa L. ssp. japonica 9522 was grown in paddy fields around  Shanghai (China) during the normal rice growing season (June–August).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: Photoperiod  treatment was started after panicle initiation and continued until all samples were  collected: LD was the natural daylight condition, with a photoperiod of ~14 h; SD  conditions were simulated by covering plants with black cloth for the last 2 h of natural  daylight to create a 12 h photoperiod.

tag: tissue

value: anther

tag: development stage

value: mitosis stages I

tag: genotype

value: wide type


title: HAEC, PS, 4hr, replicate 1

city: La Jolla

first: Shankar

last: Subramaniam

state: CA

address: 9500 Gilman Dr MC 0412

department: Bioengineering

institute: University of California, San Diego

description:
haec_ps_4hr_n1
HAEC_Count_Gene_with_GeneInfo.txt

data_processing:
Mapping of the RNA-Seq reads to human genome and transcriptome: RNA-seq fastq files were aligned to the Human Reference Genome (version hg19 / Human.B37.3) and raw gene read counts (Refgene) were generated using the Omicsoft Aligner (OSA) OShell version = 9.0.8.75, using default parameter/options and ExpressionMeasurement=Count, SearchNovelExonJunction=True.
Genome_build: Human.B37.3 (based on NCBI build 37.3)
Supplementary_files_format_and_content: HAEC_Count_Gene_with_GeneInfo.txt: Tab-delimited text file; The first nine columns contain information on the RefSeq (Refgene) genes (such as gene symbol). The remaining columns correspond to samples and contain the raw mapped read counts. _n1, _n2 and _n3 correspond to replicates 1, 2 and 3, respectively.

organism: Homo sapiens

source_name: HAEC

growth_protocol: HAECs (Cell Applications Cat# 03405A) were cultured in endothelial growth medium (Cell applications Cat#211-500) with 100 U/mL penicillin-streptomycin.

extract_protocol:
Samples for RNA sequencing analysis were collected at 1, 4, and 24 hrs after exposure to shear. Samples for RNA sequencing analysis were collected at 0 hr for the static condition.
The total RNA from HAECs were extracted by using TRizol RNA isolation reagent (Thermo Fisher, Cat#15596026). The RNA quality was assessed by RNA Integrity Numbers (RIN), using an Agilent Bioanalyzer, and all RNA samples used in this study had a RIN over 9.
The RNAs were ribo-depleted, fragmented, and random hexamer primed using Illumina TruSeq stranded mRNA sample preparation kit. Constructed cDNA library was subjected to single-ended 75-bp sequencing on Illumina Hi-seq 4000 instrument.

treatment_protocol: Pulsatile shear (PS) or oscillatory shear (OS) flows were applied to ECs with shear stresses of 12 ± 4 dyn/cm2 or 0.5 ± 4 dyn/cm2, respectively. ECs were also exposed to a “no flow” condition, and designated as a “static” condition.

value: Blood vessel

tag: cell type

value: HAEC

tag: condition

value: PS


title: AFD camt-1 mutant replicate 3

city: Klosterneuburg

first: Thanh

middle: TK

last: Vuong-Brender

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria

description: samples_f1453303.csv_DESeq_norm_read_counts.txt

data_processing:
RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis available at https://github.com/lmb-seq/PRAGUI. PRAGUI integrates RNA-seq processing packages including Trim Galore, FastQC, STAR, DESeq2, HTSeq, Cufflinks and MultiQC.
Genome_build: WS255_WBcel235
Supplementary_files_format_and_content: DESeq normalized read counts

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Neurons

growth_protocol: Synchronized worm grown on 9 cm rich peptone plates

extract_protocol:
Worms were incubated with lysis buffer containing DTT then mechanically (pipetting 12 min) and chemically (Pronase) dissociated. GFP cells were FACS-sorted
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina®

value: Neurons

tag: neuronal class

value: AFD

tag: strain name


title: SD04:00_2

source_name: the mitosis stages I anther sample at 04:00 in sort-day condition rep_2


title: AFD camt-1 mutant replicate 2


title: HAEC, PS, 1hr, replicate 3

description:
haec_ps_1hr_n3
HAEC_Count_Gene_with_GeneInfo.txt


title: AFD camt-1 mutant replicate 1


title: SD00:00_2

source_name: the mitosis stages I anther sample at 24:00 in sort-day condition rep_2


title: HAEC, PS, 1hr, replicate 2

description:
haec_ps_1hr_n2
HAEC_Count_Gene_with_GeneInfo.txt


title: BAG WT replicate 11

description: samples_6dc999f2.csv_DESeq_norm_read_counts.txt

value: WT

value: BAG


title: HAEC, PS, 1hr, replicate 1

description:
haec_ps_1hr_n1
HAEC_Count_Gene_with_GeneInfo.txt


title: BAG WT replicate 10


title: MLL-AF9/iFLT3-ITD ON Replicate 1


title: Ank_1386_HUPO_Ia

city: Wilmette

first: Richard

last: Pope

state: IL

address: 1932 Central Ave

department: Medicine

institute: Northwestern University

description: HUPO ankle synovial macrophages FH1

data_processing:
The sequencing library was demultiplexed and the quality of DNA reads was evaluated using FastQC.
Adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered
The sequenced reads were aligned to the Mus musculus genome (mm10) using STAR
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for 23,337 genes obtained from UCSC (University of California Santa Cruz; http://genome.ucsc.edu).
Raw gene expression counts were normalized to fragments per kilobase per million (FPKM) using cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample ...

source_name: Ankle joint tissue

extract_protocol:
Circulating classsic and non-classic monocytes,  and the 5 subsets of ankle synovial tissue macrophages were freshly harvested. All cell subsets were defined and sorted  by Flow-cytometric procedures. Total RNA was extracted from each sorted cell population (> 400 cell count) using Arcturus PicoPure RNA Isolation Kit.
Total RNA was employed for library construction.  Full-length cDNA synthesis and amplification were carried out with the Clontech SMART-Seq v4 Ultra Low Input RNA Kit.  Illumina sequencing libraries were prepared from the amplified full-length cDNA with the Nextera XT DNA Library Preparation Kit.The sequencing of the libraries employed an Illumina NextSeq 500 NGS System.  Single 75 bp reads were generated with dual indexing and the libraries were sequenced to an average depth of 21.8 million reads

tag: strain

tag: age

value: ≥ 21 and ≤ 37 weeks old


title: SD00:00_1

source_name: the mitosis stages I anther sample at 24:00 in sort-day condition rep_1


title: HAEC, OS, 24hr, replicate 3

description:
haec_os_24hr_n3
HAEC_Count_Gene_with_GeneInfo.txt

value: OS


title: SD04:00_1

source_name: the mitosis stages I anther sample at 04:00 in sort-day condition rep_1


title: Ank_1170_HUPO_Ia

description: HUPO ankle synovial macrophages FH1


title: SD20:00_1

source_name: the mitosis stages I anther sample at 20:00 in sort-day condition rep_1


title: BAG WT replicate 9


title: BAG WT replicate 8


title: HAEC, OS, 24hr, replicate 1

description:
haec_os_24hr_n1
HAEC_Count_Gene_with_GeneInfo.txt


title: HAEC, OS, 24hr, replicate 2

description:
haec_os_24hr_n2
HAEC_Count_Gene_with_GeneInfo.txt


title: Ank_1084_HUPO_Ia

description: HUPO ankle synovial macrophages FH1


title: SD16:00_2

source_name: the mitosis stages I anther sample at 16:00 in sort-day condition rep_2


title: Ank_1194_Control_Ia

description: Control ankle synovial macrophages FH1


title: HAEC, OS, 4hr, replicate 3

description:
haec_os_4hr_n3
HAEC_Count_Gene_with_GeneInfo.txt


title: Ank_1085_Control_Ia

description: Control ankle synovial macrophages FH1


title: BAG WT replicate 7


title: SD12:00_2

source_name: the mitosis stages I anther sample at 12:00 in sort-day condition rep_2


title: BAG WT replicate 6


title: BAG WT replicate 5


title: HAEC, OS, 4hr, replicate 1

description:
haec_os_4hr_n1
HAEC_Count_Gene_with_GeneInfo.txt


title: SD16:00_1

source_name: the mitosis stages I anther sample at 16:00 in sort-day condition rep_1


title: SD20:00_2

source_name: the mitosis stages I anther sample at 20:00 in sort-day condition rep_2


title: Ank_1167_Control_Ia

description: Control ankle synovial macrophages FH1


title: Ank_1231_HUPO_Ib

description: HUPO ankle synovial macrophages FH2


title: Ank_1170_HUPO_Ib

description: HUPO ankle synovial macrophages FH2


title: SD12:00_1

source_name: the mitosis stages I anther sample at 12:00 in sort-day condition rep_1


title: Ank_1084_HUPO_Ib

description: HUPO ankle synovial macrophages FH2


title: HAEC, OS, 4hr, replicate 2

description:
haec_os_4hr_n2
HAEC_Count_Gene_with_GeneInfo.txt


title: BAG WT replicate 4


title: SD08:00_2

source_name: the mitosis stages I anther sample at 08:00 in sort-day condition rep_2


title: HAEC, OS, 1hr, replicate 3

description:
haec_os_1hr_n3
HAEC_Count_Gene_with_GeneInfo.txt


title: HAEC, OS, 1hr, replicate 2

description:
haec_os_1hr_n2
HAEC_Count_Gene_with_GeneInfo.txt


title: Ank_1470x4_Control_Ib

description: Control ankle synovial macrophages FH2


title: Ank_1392_Control_Ib

description: Control ankle synovial macrophages FH2


title: BAG WT replicate 3


title: HAEC, OS, 1hr, replicate 1

description:
haec_os_1hr_n1
HAEC_Count_Gene_with_GeneInfo.txt


title: Ank_1085x5_Control_Ib

description: Control ankle synovial macrophages FH2


title: BAG WT replicate 2


title: BAG WT replicate 1


title: BAG camt-1 mutant replicate 10


title: HAEC, ST, 0hr, replicate 2

description:
haec_st_n2
HAEC_Count_Gene_with_GeneInfo.txt

value: ST


title: Ank_1386_HUPO_Iic

description: HUPO ankle synovial macrophages FI3


title: Ank_1231_HUPO_Iic

description: HUPO ankle synovial macrophages FI3


title: BAG camt-1 mutant replicate 9


title: HAEC, ST, 0hr, replicate 1

description:
haec_st_n1
HAEC_Count_Gene_with_GeneInfo.txt


title: bladder cancer tissue#2

type: RNA

city: Shenyang

first: Liping

last: Shan

state: Liaoning

address: 36 Sanhao street

institute: Shenjing hospital of China Medical University

description:
SAMPLE 5
micro RNAs
Test
miRNA qPCR assay

data_processing:
The normalization and all the data analysis were performed according to the manufacturer's instructions using their web-based software package: https://geneglobe.qiagen.com/au/analyze/
For the normalization it uses the average of five housekeeping genes: SNORD61, SNORD68, SNORD72, SNORD95, SNORD96A.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change file reports test/control (tumor/adjacent) ratios.

label: SYBR Green

source_name: bladder cancer tissue

label_protocol: 600 ng total RNA was used to synthesize complement DNA with the RT2 First Strand Kit (Qiagen). PCR reactions were conducted with the Mx3000P system (Thermo Fisher Scientific, Waltham, MA, US). PCR was conducted as follows: 40 cycles of 94 °C for 15s, 60 °C for 10s, and 72 °C for 20s. A comparative cycle threshold method was used to calculate each condition to control reactions. U6 was used as an internal control in miRNA RT-qPCR reactions, while GAPDH was used in mRNA RT-qPCR reactions per the 2-ΔΔCq estimation.

growth_protocol: The tumor tissues were obtained from consenting patients and were reviewed by two dependent pathologists. The fresh tumor- and the corresponding adjacent tissues were removed synchronically and stored in liquid nitrogen immediately.

extract_protocol: Total RNA was collected from fresh cells and tissues with the RNeasy Mini Kit according to the manufacturer’s protocol (Qiagen, Hilden, Germany).

value: Bladder cancer tissue

tag: gender

value: Male


title: bladder cancer tissue#3

description:
SAMPLE 6
micro RNAs
Test
miRNA qPCR assay


title: HAEC, ST, 0hr, replicate 3

description:
haec_st_n3
HAEC_Count_Gene_with_GeneInfo.txt


title: BAG camt-1 mutant replicate 8


title: Ank_1170_HUPO_Iic

description: HUPO ankle synovial macrophages FI3


title: PMC_78T_control

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

hyb_protocol: Illumina Illumina

scan_protocol: Illumina iScan System Illumina iScan System

data_processing:
Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.
Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

molecule: genomic DNA

source_name: Organoid

label_protocol:
Illumina
Illumina

extract_protocol:
Extraction of high molecular weight DNA from frozen tumor samples was carried out using Promega ReliaPrep™ gDNA Tissue Miniprep System
Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany) after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany).

value: malignant rhabdoid tumor organoid

tag: material

value: Frozen

tag: tumor subgroup

value: MRT


title: PMC_103T_control


title: adjacent tissue#3

description:
SAMPLE 3
micro RNAs
Control
miRNA qPCR assay

source_name: adjacent tissue

value: Non-cancerous tissue


title: bladder cancer tissue#1

description:
SAMPLE 4
micro RNAs
Test
miRNA qPCR assay


title: melanoma_K484_blood_VDJ

first: Osmaan

last: Shahid

address: 77 Avenue Louis Pasteur

department: Department of Immunology

institute: Harvard Medical School

description:
Cells were sort-purified as live, singlet, CD45+CD3+ and loaded into a single channel
processed data file: K484_Blood.rds
K484_Blood_TCR

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and csv files of TCR clonality were performed using the Cell Ranger analysis pipeline (v3.0.2)
Data normalization, dimension reduction, and differential expression analysis were performed using R version 3.6.1 and the Seurat R package (version 3)
When applicable, samples were integrated using the SCTransform Method (Hafemeister and Satija, 2019, Genome Biol 20:196)
Genome_build: GRCh38
Supplementary_files_format_and_content: .rds files contain Seurat objects with the count matrix as an RNA assay, and the TCR data, matching status, and other data in the @meta.data field.

source_name: human melanoma

growth_protocol: Live cells were sort-purified using an BD FACSAria Fusion (BD Biosciences) from collagenase-digested human melanoma samples or from PBMCs isolated by Ficoll gradient

extract_protocol:
Cells from tumor samples and peripheral blood were loaded into the 10X Chromium Controller using the Chromium Single Cell 5' Library and Gel Bead Kit (10X Genomics)
For samples with gene expression and T cell receptor sequencing, the Chromium Single Cell V(D)J protocol was used.
10X Chromium Single Cell V(D)J kits (5' gene expression with paired T cell receptor sequencing)

treatment_protocol: The initial paired blood/tumor samples were from checkpoint therapy-naïve metastatic melanoma patients. The two follow up (longitudinal) blood samples (patient K411 and patient K468) were post checkpoint therapy. Patient K468 received anti-PD-1 and anti-CTLA-4 therapy, and the longitudinal sample was taken one month into treatment. Patient K411 received anti-PD-1 followed by pIL-12 (TAVO) plus anti-PD-1 treatment. The longitudinal blood sample was taken about 16 months after the initial sample.

tag: site

value: peripheral blood

tag: treatment status

value: naïve

tag: time point

value: initial paired blood/tumor sample from patient K484, checkpoint therapy naïve


title: BAG camt-1 mutant replicate 7

description: samples_6dc999f2.csv_DESeq_norm_read_counts.txt

source_name: Neurons


title: melanoma_K484_blood_GEX

description:
Cells were sort-purified as live, singlet, CD45+CD3+ and loaded into a single channel
K484_Blood_GEX


title: Ank_1470x4_Control_Iic

description: Control ankle synovial macrophages FI3


title: adjacent tissue#2

description:
SAMPLE 2
micro RNAs
Control
miRNA qPCR assay


title: Ank_1167_Control_Iic

description: Control ankle synovial macrophages FI3


title: PMC_60T_smarcb1


title: BAG camt-1 mutant replicate 6


title: melanoma_K484_LN_met_VDJ

description:
Cells were sort-purified as live, singlet, CD45+CD3+ and loaded into a single channel
processed data file: K484_Tumor.rds
K484_Tumor_TCR

value: Involved regional lymph node


title: melanoma_K484_LN_met_GEX

description:
Cells were sort-purified as live, singlet, CD45+CD3+ and loaded into a single channel
K484_Tumor_GEX


title: Ank_1085_Control_Iic

description: Control ankle synovial macrophages FI3


title: Ank_1386_HUPO_Iib

description: HUPO ankle synovial macrophages FI2


title: BAG camt-1 mutant replicate 4

value: Neurons


title: IFN-γ 44_Ctrl_miR_2

city: Guangzhou

first: Emmanuel

middle: E

last: Dzakah

state: Guangdong

address: Lujing Lu, Yuexiu District

institute: Dermatology Hospital

description: miR-seq data of HeLa cells in the presence of IFN-γ at 44 hrs

data_processing:
Zebra call software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200, and RSEM v1.2.12  with parameters --forward-prob 0.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from   Langmead and Salzberg, Nat Methods, 2012. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.  Li and Dewey， BMC Bioinformatics, 2011.Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: cervix

growth_protocol: Cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (Sigma-Aldrich, USA) at 37℃ with 5% CO2.

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with C. trachomatis serovar E at multiplicity of infection of 1 after treatment with DEAE-Dextran.

value: cervix

tag: cell line

value: IFN-ɣ treatment for 44hrs


title: BAG camt-1 mutant replicate 5

value: BAG


title: adjacent tissue#1

description:
SAMPLE 1
micro RNAs
Control
miRNA qPCR assay


title: A223-WES

city: Aurora

first: Jing

middle: Hong

last: Wang

state: Colorado

address: 12800 East 19th Ave, Mail stop 8333, RC1 North, Room 9400C

department: Immunology and Microbiology

institute: University of Colorado at Anschutz

description: Exonic DNA

library_source: genomic

data_processing:
see Woolaver et al. 2021 methods (Journal for Immunotherapy of Cancer)
Supplementary_files_format_and_content: variants from A223 whole-exome sequencing and RNA sequencing mapped to C57BL/6 genome using BWA, variant calling and filtering using GATK, and annotation using snpEff.

source_name: Tumor cells

growth_protocol: (2) A223 tumor cells were grown in vitro

extract_protocol:
(2) RNA and DNA were isolated from A223 cells grown in vitro
(2) RNA: Libraries were prepared for sequencing using standard Illumina protocols.
(2) DNA: Qualified genomic DNA samples were randomly sheared by the ultrasonic highperformance sample processing system (Covaris) into fragments with a main peak of about 200bp-300bp. Subsequently, repaired the end of DNA fragment, added nucleotide A at 3' end, and ligated adapters at both ends. The library ligated with adapters were linearly amplified (LM-PCR) to produce a hybrid library. Took an appropriate amount of hybrid library for capture and enrichment with exon chip, and eluted the unenriched fragments followed by amplification. The amplified products were subjected to QPCR quality control, qualified products were for sequencing.
(2) RNA: bulk RNA sequencing
(2) DNA: Whole-exome sequencing

tag: tumor state

value: In vitro

value: Tumor

tag: experiment

value: (2) A223 variant analysis


title: melanoma_K468_longitudinal_blood_VDJ

description:
Cells were sort-purified as live, singlet, CD45+CD3+CD8+ and loaded into a single channel
processed data file: K468_Blood_Longitudinal.rds
K468_Blood_Longitudinal_TCR

value: post-treatment

value: longitudinal blood sample fro patient K468, collected after the initial paired blood/tumor sample and after onset of checkpoint blockade


title: Ank_1231_HUPO_Iib

description: HUPO ankle synovial macrophages FI2

source_name: Ankle joint tissue

value: ≥ 21 and ≤ 37 weeks old


title: PMC_103T_smarcb1

tag: tissue

value: malignant rhabdoid tumor organoid

value: Frozen


title: BAG camt-1 mutant replicate 3

tag: genotype


title: IFN-γ 44_Ctrl_2

description: RNA-seq data of HeLa cells in the presence of IFN-γ at 44 hrs

tag: treatment


title: melanoma_K468_longitudinal_blood_GEX

description:
Cells were sort-purified as live, singlet, CD45+CD3+CD8+ and loaded into a single channel
K468_Blood_Longitudinal_GEX


title: Ank_1170_HUPO_Iib

description: HUPO ankle synovial macrophages FI2


title: PMC_78T_smarcb1

value: MRT


title: BAG camt-1 mutant replicate 2

tag: cell type


title: IFN-γ 44_Ctrl_1

description: RNA-seq data of HeLa cells in the presence of IFN-γ for 44 hrs


title: melanoma_K468_blood_VDJ

description:
Cells were sort-purified as live, singlet, CD45+CD3+CD8+ and loaded into a single channel
processed data file: K468_Blood.rds
K468_Blood_TCR

value: peripheral blood

value: initial paired blood/tumor sample from patient K468, checkpoint therapy naïve


title: Ank_1386_HUPO_Iia

description: HUPO ankle synovial macrophages FI1


title: BAG camt-1 mutant replicate 1

tag: neuronal class


title: melanoma_K468_blood_GEX

description:
Cells were sort-purified as live, singlet, CD45+CD3+CD8+ and loaded into a single channel
K468_Blood_GEX

value: naïve


title: Ank_1231_HUPO_Iia

description: HUPO ankle synovial macrophages FI1


title: RMG WT replicate 4

description: samples_00bfd18d.csv_DESeq_norm_read_counts.txt

value: WT

value: RMG

tag: strain name


title: RMG WT replicate 3

value: Neurons


title: IFN-γ 44hpi__miR_1

description: miR-seq data of Chlamydia trachomatis-infected HeLa cells at 44 hrs post-infection in the presence of IFN-γ

value: cervix

value: C. trachomatis infection for 44hrs in the presence of IFN-ɣ


title: melanoma_K468_subcu_met_GEX

description:
Cells were sort-purified as live, singlet, CD45+CD3+ and loaded into a single channel
K468_Tumor_GEX

value: axillary subcutaneous metastasis


title: IFN-γ 44hpi__miR_2


title: IFN-γ 44_Ctrl_miR_1

value: IFN-ɣ treatment for 44hrs


title: Ank_1392_Control_Iia

description: Control ankle synovial macrophages FI1

tag: strain


title: melanoma_K411_longitudinal_blood_VDJ

description:
Cells were sort-purified as live, singlet, CD45+CD3+CD8+ and loaded into a single channel
processed data file: K411_Blood_Longitudinal.rds
K411_Blood_Longitudinal_TCR

value: longitudinal blood sample from patient K411, collected after the initial paired blood/tumor sample and after onset of checkpoint blockade


title: IFN-γ 44hpi_1

description: RNA-seq data of Chlamydia trachomatis-infected HeLa cells at 44 hrs post-infection in the presence of IFN-γ


title: Ank_1194_Control_Iia

description: Control ankle synovial macrophages FI1

tag: age


title: RMG WT replicate 1


title: RMG WT replicate 2


title: 44hpi__miR_2

description: miR-seq data of Chlamydia trachomatis-infected HeLa cells at 44 hrs post-infection

value: C. trachomatis infection for 44hrs


title: IFN-γ 44hpi_2


title: 44hpi__miR_1


title: melanoma_K411_blood_VDJ

description:
Cells were sort-purified as live, singlet, CD45+CD3+CD4-CD8+ and  CD45+CD3+CD4+CD8- loaded into a single channel in a 60:40 ratio
K411_Blood_TCR

value: initial paired blood/tumor sample from patient K411, checkpoint therapy naïve


title: Ank_1167_Control_Iia

description: Control ankle synovial macrophages FI1

value: ≥ 21 and ≤ 37 weeks old


title: melanoma_K411_longitudinal_blood_GEX

description:
Cells were sort-purified as live, singlet, CD45+CD3+CD8+ and loaded into a single channel
K411_Blood_Longitudinal_GEX

value: post-treatment


title: Bld_1739_HUPO_NC

description: HUPO circulating non-classical monocytes

source_name: Blood


title: melanoma_K411_LN_met_VDJ

description:
Cells were sort-purified as live, singlet, CD45+CD3+CD4-CD8+ and  CD45+CD3+CD4+CD8- loaded into a single channel in a 80:20 ratio
K411_Tumor_TCR

value: Involved regional lymph node


title: 44hpi_2

description: RNA-seq data of Chlamydia trachomatis-infected HeLa cells at 44 hrs post-infection


title: melanoma_K468_subcu_met_VDJ

description:
Cells were sort-purified as live, singlet, CD45+CD3+ and loaded into a single channel
processed data file: K468_Tumor.rds
K468_Tumor_TCR


title: RMG camt-1 mutant replicate 4


title: Bld_1606_HUPO_NC


title: Ank_1170_HUPO_Iia

description: HUPO ankle synovial macrophages FI1


title: RMG camt-1 mutant replicate 2


title: PMC_60T_control

value: malignant rhabdoid tumor organoid

value: Frozen

value: MRT


title: melanoma_K409_blood_VDJ

description:
Cells were sort-purified as live, singlet, CD45+CD3+CD4-CD8+ and loaded into a single channel
K409_Blood_TCR

value: peripheral blood

value: naïve

value: initial paired blood/tumor sample from patient K409, checkpoint therapy naïve


title: Bld_1505_HUPO_NC


title: RMG camt-1 mutant replicate 1

value: Neurons

value: RMG


title: Input_L

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

country: France

institute: UMR9002 CNRS-UM

data_processing:
Raw reads filtering perfomed with fastq_illumina_filter (version 0.1)
Raw reads quality control perfomed with Fastqc (version 0.11.2)
Reads alignment with BWA (0.7.10) on HG38 human genome version
Bigwig files were generated using deeptools (3.2.0) bamCompare and normalized either by corresponding input or by the average of four inputs (subtraction) using RPGC normalization
Genome_build: HG38
Supplementary_files_format_and_content: bigwig files containing ChIP-seq coverage for each sample normalized by the corresponding input

source_name: HeLa cell

growth_protocol: HeLa cells were grown in Dulbecco modified Eagle's minimal essential medium (DMEM) (sigma-Aldrich D6429), supplemented with 10% FCS, and containing 1% Penicillin streptomycin (Sigma P4333). All cells were grown in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
ChIP experiments were performed in HeLa cells using the ChIP IP High Sensitivity (Active Motif 53040).
ChIP-seq librairies were constructed using the Next Gen DNA Library Kit

treatment_protocol:
MRN complex was depleted by transducing HeLa cells with shRNA expressing lentiviral particles for 4 days.
Heat shock was performed on HeLa cells by incubating the celss for one hour at 42°C
RNAPII build up was performed by treating HeLa cells with 150µM DRB for 0, 1 or 3h as indicated. "Release" samples were treated for 3h with DRB then washed and harvested after 1h of incubation at 37°C

tag: passages

tag: chip antibody


title: 20hpi__miR_2

description: miR-seq data of Chlamydia trachomatis-infected HeLa cells at 20 hrs post-infection

value: cervix

value: C. trachomatis infection for 20hrs


title: 44hpi_1


title: Bld_1508_Control_NC

description: Control circulating non-classical monocytes


title: 20hpi__miR_1


title: Bld_1506_Control_NC


title: L_PolII

value: Santa Cruz 55492


title: RMG camt-1 mutant replicate 3


title: Sensory neurons (URX/AQR/PQR) WT replicate 4

description: samples_ed0924f5.csv_DESeq_norm_read_counts.txt

value: WT

value: URX/AQR/PQR


title: Bld_1470_Control_NC


title: Sensory neurons (URX/AQR/PQR) WT replicate 3


title: Bld_1739_HUPO_C

description: HUPO circulating classical monocytes


title: 20hpi_1

description: RNA-seq data of Chlamydia trachomatis-infected HeLa cells at 20 hrs post-infection


title: L_NBS1

value: Bethyl A300-289A


title: L_MRE11

value: Bethyl A303-998A


title: Sensory neurons (URX/AQR/PQR) WT replicate 2


title: 20hpi_2


title: NC__miR_1

description: miR-seq data of untreated HeLa cells, NC represents negative control

value: untreated


title: Bld_1606_HUPO_C

description: HUPO circulating classical monocytes

value: ≥ 21 and ≤ 37 weeks old


title: Bld_1505_HUPO_C

description: HUPO circulating classical monocytes


title: pheochromocytoma 4

city: Neuherberg

first: Natalia

middle: S.

last: Pellegata

address: Ingolstädter Landstr.1

institute: HMGU

data_processing:
Mapping hisat2 v2.0.5 --dta --phred33 Mapping to a reference
Qualtiy control on raw data
Filtering of clean reads, without adapater reads
HISAT2 is selected to map the filtered sequenced reads to the reference genome Rn0.6 rattus norvegicus
Quantification FeatureCounts v1.5.0-p3 Paramaeter Default
Genome_build: Rn0.6
Supplementary_files_format_and_content: differentially expressed genes

organism: Rattus norvegicus

source_name: adrenal medulla, chromaffin cells

growth_protocol: not applicable

extract_protocol:
snap-frozen, macrodissected Tissue was homogenized with a pestle and total RNA was extracted according to the protocol of the Promega Maxwell 16 LEV simplyRNA kit using the automated Maxwell 16 instrument.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNALibrary Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA waspurified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First StrandSynthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesiswas subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp inlength, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers andIndex (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

treatment_protocol: not applicable

value: Sprague-Dawely

value: 7-9,5 months

value: pheochromocytoma

value: MENX


title: pheochromocytoma 5


title: Sensory neurons (URX/AQR/PQR) WT replicate 1


title: SD08:00_1

source_name: the mitosis stages I anther sample at 08:00 in sort-day condition rep_1

value: anther

tag: development stage

value: mitosis stages I

value: wide type


title: pheochromocytoma 3


title: pheochromocytoma 2


title: Sensory neurons (URX/AQR/PQR) camt-1 mutant replicate 5

value: Neurons


title: Bld_1508_Control_C

description: control circulating classical monocytes


title: Sensory neurons (URX/AQR/PQR) camt-1 mutant replicate 4


title: NC_2

description: RNA-seq data of untreated HeLa cells, NC represents negative control

value: cervix


title: Bld_1506_Control_C

description: Control circulating classical monocytes


title: Sensory neurons (URX/AQR/PQR) WT replicate 5


title: Sensory neurons (URX/AQR/PQR) camt-1 mutant replicate 3


title: pheochromocytoma 1


title: Bld_1470_Control_C

description: Control circulating classical monocytes


title: hyperplastic adrenal medulla 5

value: 4-5 months

value: hyperplastic adrenal medulla


title: Sensory neurons (URX/AQR/PQR) camt-1 mutant replicate 1


title: Sensory neurons (URX/AQR/PQR) camt-1 mutant replicate 2


title: NC__miR_2


title: SPi

city: Trondheim

first: Luciana

last: Fernandes de Brito

address: Kjemi 3, 3.237, Gløshaugen, Sem Sælandsvei 6/8

department: Department of Biotechnology and food science

country: Norway

institute: Norwegian University of Science and Technology

data_processing:
To prepare the reads for mapping, the tool Trimmotatic version 0.33 (DOI: 10.1093/bioinformatics/btu170) was used to trim the sequences to a minimal length of 35 base pairs.
The sequence reads were mapped onto the reference genome of P. sonchi genomovar Riograndensis SBR5 (GenBank LN831776).
Trimmed reads were mapped to the reference genome of SBR5 through the software for short read alignment Bowtie (DOI: 10.1002/0471250953.bi1107s32).
The visualization of mapped reads and the differential gene expression analysis were performed using the software ReadXplorer (DOI: 10.1093/bioinformatics/btu205), in which the statistical method DEseq was employed to analyze the resultant RNAseq data (DOI: 10.1186/gb-2010-11-10-r106).
The cut-off values for designating a gene as differentially expressed included a change in expression level (base mean) higher than 30 and an adjusted P-value of equal to or less than 0.05.

organism: Paenibacillus riograndensis

source_name: Soluble phosphate source

growth_protocol: One mL of the bacterial suspension was inoculated into 500 mL shaking flasks containing 50 mL of distinct broth media differing with regard to the P source: 1) Pikovskaya broth (PVK) with 5 g L-1 of Ca5(PO4)3(OH) (hydroxyapatite) as P source (IPi); 2) PVK with 3.2 g L-1 NaH2PO4 as P source (SPi). To maintain neutral pH of both media, 12 g L-1 of 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid (HEPES) were added. The cells grown in each condition were used to re-inoculate fresh media. For each condition tested, six biological replicates were used: three for total RNA isolation, and three for further determination of growth characteristics. Bacterial cells of three replicate cultivations were harvested after 6 hours of growth, in the middle of the exponential phase, and the harvesting procedure was done according to Irla et al. (DOI: 10.1186/s12864-015-1239-4).

extract_protocol:
All the procedures regarding RNA isolation and RNA quality control were done according to Brito et al. (DOI: 10.1186/s12864-017-4235-z).
The three replicates of extracted RNA samples of each condition were pooled in equal parts and the pool of total RNA was subsequently used for the preparation of cDNA libraries. For each condition, a whole transcriptome library was prepared. For removal of ribosomal RNA, Ribo-Zero Plus rRNA Depletion Kit (Illumina, San Diego, USA) was used according to manufacturer’s recommendations. The preparation of this library and the cDNA sequencing were carried out according to Mentz et al. (DOI: https://doi.org/10.1186/1471-2164-14-714).

tag: material

value: Cell pellets- shake flask cultivation

value: Wild type


title: hyperplastic adrenal medulla 4


title: RCdM5_2

city: Chengdu

first: Jiyun

last: Peng

state: Sichuan

address: Huimin Road 211,Wenjiang District

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: https://www.ncbi.nlm.nih.gov/nuccore/NBSK00000000.1/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Lactuca sativa

source_name: roots

extract_protocol:
The leaves and roots were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Italian Lettuce (Lactuca sativa L. var. ramose Hort.) seeds were sterilized with 10 % hydrogen peroxide for 10 min and rinsed thoroughly with distilled water for three times, then germinated on moist filter paper in the dark at 20 °C. After the initiation for 0.5 cm, the seeds were transferred to a salver (40 x 30 cm) filled with perlite and covered by vermiculite for moisture holding. Then, they were transferred into the incubator under 23℃/18℃ for 14h/10h in day and night time, respectively. The relative humidity set as 70% and the light intensity was 15,000 lx. After the formation of seedlings, they were watered with 200ml half-strength Hoagland’s nutrient solution per day for 20 days, subsequently cultivated in a growth chamber. 20 days later, the seedlings were divided into two groups: 1) seedlings cultivated with the nutrient solution with 1μmol/L (Sigma-Aldrich, USA) melatonin. 2) seedlings cultivated with the nutrient solution without melatonin. Then, these two groups were treated by 50 μmol/L CdCl2 for simulation a Cd stress environment, and the nutrient solution was replenished regenerated once for three days to maintain constant concentrations. The leaves and root of 0d, 1d, and 5d seedlings in two groups have been sampled, and three biological repeats were included for each treatment . All samples were stored in Ultra-low Temperature Freeze under -80° before conducting.

tag: type

value: Italian Lettuce

value: roots

value: 20 days+5 days to treated by 50 μmol/L CdCl2 and 1μmol/L melatonin


title: RCdM5_3

growth_protocol: Italian Lettuce (Lactuca sativa L. var. ramose Hort.) seeds were sterilized with 10 % hydrogen peroxide for 10 min and rinsed thoroughly with distilled water for three times, then germinated on moist filter paper in the dark at 20 °C


title: hyperplastic adrenal medulla 3


title: Eto_LTi_rep1

city: Beijing

first: Chao

last: Zhong

address: 38 Xueyuan Rd , Haidian District

department: Institute of Systems Biomedicine

institute: Peking University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were mapped to the mouse (mm10) genomes with hisat2 (2.1.0) with default settings. We kept one hit if multiple reads were mapped to the same position for each RNA-Seq libraries.
For each RNA-Seq sample, gene expression was quantified using featureCounts function in Subread package.
Genome_build: mm10
Supplementary_files_format_and_content: read count: plan text file. Columns from left to right denote ENSEMBL ID, chromosome, start, end,strand,exon length,number of read mapped to exons.

source_name: LTi treated by Etomoxir

extract_protocol:
(GA9551-GA9558): Single cell suspension were obtained from the colon lamina propria of C57BL/6 mice. For sorting huPD-1high LTi and huPD-1- LTi cells, cells were stained with relative antibodies followed by sorting on a BD Aria III cell sorter for  "live Lineage-CD127+KLRG-1-c-Kit+CCR6+huPD-1high" and "live Lineage-CD127+KLRG-1-c-Kit+CCR6+huPD-1-" cells.  (C-4, C-6, E-5, E-6): Single cell suspension were obtained from the small intestinal lamina propria of Pdcd1-/-Rag2-/- mice. For sorting LTi cells, cells were stained with relative antibodies followed by sorting on a BD Aria III cell sorter for  "live Lineage-CD127+KLRG-1-c-Kit+CCR6+"
The sorted LTi were collected in lysis buffer of the SMART-Seq HT Kit (Takara) followed with cDNA synthesis and amplification according to the manufacturer’s protocols. Sequencing libraries were generated using NEB Next Ultra DNA Prep Kit (New England Biolabs), according to the manufacturer’s instruction. Libraries were assessed using the Agilent 2100 Bioanalyzer system and sequenced by paired-end 150 base pair reads using the Illumina NovaSeq platform.

treatment_protocol: (GA9551-GA9558): Age-matched adult Pdcd1hu/+ mice and Pdcd1hu/- mice were administratedfed with 3% (w/v) DSS  in their drinking water for 6 days, followed with recovery by DSS withdrawal for 1 day.   (C-4, C-6, E-5, E-6): LTi were sorted from adult Pdcd1-/-Rag2-/- mice. The sorted LTi were cultured with palmitic acid and L-Carnitine and  treated with 60 µM Etomoxir or vehicle (H2O) for the first two days and 200 µM Etomoxir or vehicle (H2O) for the next two days.

tag: isolate

value: isolated from small intestinal lamina propria lymphocytes

tag: in vitro treatment

value: Etomoxir


title: RCdM5_1


title: CnR_SALL4_nuc_repl3

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

data_processing:
library strategy: CUT&RUN
Cut&Run - Cut and Run Analysis Pipeline (CnRAP) scripts can be found on github (https://github.com/mbassalbioinformatics/CnRAP).  Raw fastq files were trimmed with Trimmomatic (REF, v0.36 tested) in paired end mode with the flags “ILLUMINACLIP: <adapter_path> Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25”. Next, the kseq trimmer developed by the Orkin lab was run on each fastq file, there were no flags to modify.  For alignment, BWA (v0.7.17-r1188 tested) was first run in “aln” mode on a masked hg38 genome downloaded from UCSC to create *.sai files.  Next, BWA was run in “sampe” mode with the flag “-n 20” on the *.sai files.  Afterwards, stampy (v1.0.32 tested) was run in “--sensitive" mode.  For mapping statistics, bamtools (v2.5.1 tested) “stat” was used.  Post alignment, unmapped reads were removed from bam files using bamtools with the flags “filter -isMapped true.”  Next, using samtools (v1.5 tested), bam files were sorted (“sort -l 9 -O bam”), had read pair mates fixed (“fixmate”) and indexed (“index”).  Bam coverage maps were generated using bamCoverage from the deeptools suite (v2.5.7 tested).  The same procedure was run to align fastq files to a masked genome Saccharomyces Cerevisiae v3 (sacCer3), also downloaded from UCSC.    In preparation for peak calling, a normalization factor was determined for each hg38 aligned replicate based on the corresponding number of proper-pairs aligned to the sacCer3 genome, as recommended in the Henikoff pipeline.  This was calculated as follows  normalization_factor=10,000,000\(#proper_pairs/2).  The number of ‘proper-pairs’ was extracted from the bamtools mapping statistics calculated previously. Next, from the hg38 aligned bams, ‘proper-paired’ reads were extracted using samtools with the flags “view -b -f 2 -F 524” with the output piped into bedtools with the flags “genomecov -bg -scale <normalization_factor> -ibam stdin.”  This produced bed files of ‘proper-paired’ reads that have been normalized to the number of reads aligned back to the sacCer3 genome.  Bedgraphs of these normalized bed files were generated as intermediary files to facilitate generation of bigwig coverage maps using the bedGraphToBigWig from UCSC (v4).  For peak calling, the recently developed SEACR (v1.1 tested) was utilized and run in both “stringent” and “relaxed” mode to produce peak files with the flag “non” as the bed files were already normalized to the number of yeast spike-in reads.  Subsequently peak file columns were re-arranged to facilitate motif discovery using both HOMER (v4.10 tested, flags “-size given,50,100,200 -mask -p 20 -S 50”) and MEME (v5.0.5 tested, “-dreme-m 50 -meme-nmotifs 50”).  Peaks were annotated using the R package ChIPSeeker (v1.20.0 tested).  Overlapping peak subsets were generated using mergePeaks.py from the HOMER suite with the flag “-d 1000”.
NicE-seq - Raw fastq reads were trimmed and mapped in the same way as described above for CUT&RUN data. Peaks were called with Model-based Analysis of ChIP-seq (MACS) (v2.1.1.20160309) for scrambled control sample and SALL4 KD sample separately. Unique peaks to each sample was identified with HOMER mergePeaks function. bamCoverage (described above for CUT&RUN) was used to generate BigWig files for visualization.
RNA-Seq - The raw fastq reads were trimmed using TrimGalore (v.0.4.5) and mapped to hg38 genome downloaded from UCSC using STAR. The read counts table was generated with the featureCounts. Differential gene expression analysis was performed to compare scrambled control samples with SALL4 KD samples using DESeq2 and the fold change was plotted as a volcano plot using ggplot2.
Genome_build: (human) hg38, (yeast) saccer3
Supplementary_files_format_and_content: peak files; gene x features expression matrix tab delimited text

growth_protocol: SNU398 cells were grown in RPMI media with 10% FBS

extract_protocol:
Briefly, 2 million cell nuclei were immobilized on Concanavalin A beads after washing. SALL4 (CST D16H12) or normal rabbit IgG (Cell Signaling DA1E) were incubated with the nuclei overnight in the presence of 0.02% digitonin at 4 degrees. The next day, 700ng/mL of proteinA-micrococcal nuclease (pA-Mnase purified in house with vector from Addgene 86973, protocol from Schmid et al.) were incubated with the nuclei at 4 degrees for an hour. After washing, the tubes were  laced in heat blocks on ice set to 0 degrees, CaCl2 (1mM) was added and incubated for 30 minutes before 2x Stop buffer containing EDTA was added. DNA was eluted by heat and highspeed spin, then phenol-chloroform extracted.
NEBNext Ultra II DNA library prep kit (NEB E7645) was used to make the libraries according to Liu et al.’s protocol, outlined on protocols.io (dx.doi.org/10.17504/protocols.io.wvgfe3w)
Pair-end (42bp) Illumina sequencing was performed on the barcoded and amplified libraries

tag: cell line

value: Hepatocellular Carcinoma cell line

tag: chip anitbody

value: SALL4 (CST D16H12)

tag: molecule subtype

value: nuclear extract


title: Ctrl_LTi_rep2

source_name: LTi treated by vehicle (H2O)

value: Vehicle (H2O)


title: Eto_LTi_rep2


title: CnR_SALL4_nuc_repl2


title: NC_1

tag: tissue

value: untreated


title: RCd5_3

tag: treatment

value: 20 days+5 days to treated by 50 μmol/L CdCl2


title: CnR_SALL4_nuc_repl1

tag: cell type


title: hyperplastic adrenal medulla 2

value: Sprague-Dawely

tag: genotype

value: MENX


title: RCd5_2


title: Ctrl_LTi_rep1


title: CnR_igg_repl3

value: normal rabbit IgG (Cell Signaling DA1E)


title: Normal adrenal medulla 5

value: 7-9,5 months

value: Normal adrenal medulla

value: wildtype


title: A223-RNA

description: polyA RNA

data_processing: Supplementary_files_format_and_content: variants from A223 whole-exome sequencing and RNA sequencing mapped to C57BL/6 genome using BWA, variant calling and filtering using GATK, and annotation using snpEff.

tag: tumor state

value: In vitro

value: Tumor

tag: experiment

value: (2) A223 variant analysis


title: CnR_igg_repl2


title: IPi

source_name: Insoluble phosphate source

tag: strain

value: Cell pellets- shake flask cultivation

value: Wild type


title: RCd5_1

value: Italian Lettuce

value: roots


title: Normal adrenal medulla 4

tag: age


title: Growing3-Spln-VDJ

description: polyA RNA 5' capture VDJ enriched

data_processing:
see Woolaver et al. 2021 methods (Journal for Immunotherapy of Cancer)
Supplementary_files_format_and_content: CellRanger output files
Supplementary_files_format_and_content: Raw counts per gene for CD8 T cells in the 9 RNA expression samples (Grow1-TIL, Grow2-TIL, Grow3-TIL, Regr1-TIL, Regr2-TIL, Regr3-TIL, Regr2-Spln, Regr3-Spln, Grow3-Spln)
Supplementary_files_format_and_content: Normalized counts per gene for CD8 T cells in the 9 RNA expression samples (Grow1-TIL, Grow2-TIL, Grow3-TIL, Regr1-TIL, Regr2-TIL, Regr3-TIL, Regr2-Spln, Regr3-Spln, Grow3-Spln)
Supplementary_files_format_and_content: Metadata for CD8 T cells in the 9 samples (original sample identity, cluster identity, TCR clonotype if available, etc.)

source_name: T cells

growth_protocol: (1) A223 tumors were injected into C57BL/6J mice

extract_protocol:
(1) A223 tumors were removed from mice, digested using liberase into a single-cell suspension, and flow-sorted for CD8 T cells.
(1) Single-cell gene expression libraries were prepared using Chromium Single Cell 5’ Library & Gel Bead Kit (#1000014) or Chromium Single Cell 3’ Library & Gel Bead Kit (#1000092) according to the manufacturer’s instructions. 5' libraries were split in half, one for sequencing and another half was enriched for TCR sequencing using the Chromium Single Cell V(D)J Enrichment Kit (Mouse T Cell).
(1) Single-cell RNA sequencing

value: Growing/Progressor

value: Spleen

value: (1) single-cell RNA sequencing


title: CnR_igg_repl1

value: Hepatocellular Carcinoma cell line

value: nuclear extract


title: Normal adrenal medulla 3

value: Sprague-Dawely


title: RCdM1_3

value: 20 days+1 days to treated by 50 μmol/L CdCl2 and 1μmol/L melatonin


title: RCdM1_2

value: 21 days+1 days to treated by 50 μmol/L CdCl2 and 1μmol/L melatonin


title: RNA3 - ABCC1(WT)3

city: Phoenix

first: Matthew

last: Huentelman

state: AZ

address: 445 N Fifth Street

department: Neurogenomics

institute: Translational Genomics Research Institute

data_processing:
fastqs generated with bcl2fastq v2.18
reads  aligned with STAR v2.7.3a
abundance measurements obtained with featureCounts from Subread package v2.0.0
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file includes sequenced exon counts

source_name: neuroblastoma cells

growth_protocol: 1.4E07 cells plated in an uncoated well of a 6-well plate in 3.0mL equal parts EMEM (ATCC, Manassas, VA, USA) and Ham's F-12 Nutrient Mix (Gibco, Thermo Fisher Scientific, Waltham,  MA) supplemented with 10% FBS (Gibco). Media changed daily until the fourth day when RNA was extracted.

extract_protocol:
Zymo Quick-RNA miniprep kit
SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio Inc., Kusatsu, Shiga, Japan)

tag: exogenous vectors

value: pSBbi-Hyg-APP, pSBbi-Pur-ABCC1(WT)


title: Regressing3-Spln-VDJ

description: polyA RNA 5' capture VDJ enriched

value: Regressing/Regressor


title: Normal adrenal medulla 2

value: 7-9,5 months

value: Normal adrenal medulla

value: wildtype


title: RNA3 - ABCC1(WT)2


title: Growing3-TIL-VDJ

description: polyA RNA 5' capture VDJ enriched

value: Tumor


title: Regressing2-Spln-VDJ

description: polyA RNA 5' capture VDJ enriched


title: hyperplastic adrenal medulla 1

value: 4-5 months

value: hyperplastic adrenal medulla

value: MENX


title: RNA3 - ABCC1(WT)1


title: Normal adrenal medulla 1


title: RCd1_3

value: Italian Lettuce

value: roots

value: 20 days+1 days to treated by 50 μmol/L CdCl2


title: S18

city: Dunsany

first: Dayle

last: Johnston

state: Ireland

address: AGRIC

department: Animal and Bioscience Research Department

country: Ireland

institute: Teagasc

data_processing:
Sequence reads were 3' trimmed for Nextera adapters, low quality reads (quality score < 20), ambiguous nucleotides, and poly-G artefacts resulting from the NextSeq’s  two-colour chemistry, using CutAdapt (version 1.18).
Reads were aligned to the UMD3.1 bovine reference genome assembly using Bowtie2 (version 2.3.4)
Mitochondrial reads, reads with a MAPQ < 10 and reads which did not align to the reference genome were removed using Samtools (version 1.9)
Peak calling (q < 0.01) was performed with MACS2 (version 2.1.4), using the BAMPE model and removing all duplicate reads.
Genome_build: UMD3.1
Supplementary_files_format_and_content: narrowPeak files output from MACS2 which provides called peaks of signal enrichment

organism: Bos taurus

source_name: bronchial lymph node

extract_protocol:
Bronchial lymph node tissue was lysed using a tissue dounce, and nuclei were obtained by density centrifugation. Nuclei were counted with a light microscope and 50,000 were used for library preparation.
ATAC-Seq libraries were prepared from 2mg of fresh BLN tissue according to the Corces, et al. (2017) “Omni-ATAC” protocol with a modification of the transposase enzyme quantity (5µl)

value: BRSV challenged

tag: breed

value: Holstein-Friesian

tag: shed

value: C

tag: tissue state

value: Fresh


title: RCd1_2

tag: type


title: RCdM1_1

value: 20 days+1 days to treated by 50 μmol/L CdCl2 and 1μmol/L melatonin


title: Regressing3-TIL-VDJ

description: polyA RNA 5' capture VDJ enriched

value: (1) single-cell RNA sequencing


title: Regressing2-TIL-VDJ

description: polyA RNA 5' capture VDJ enriched

value: Regressing/Regressor


title: S17


title: RCd1_1


title: RNA3 - Puro2

value: pSBbi-Hyg-APP, pSBbi-Pur


title: RCdM0_3

value: 20 days+0 days to treated by 50 μmol/L CdCl2 and 1μmol/L melatonin


title: S16


title: S15


title: Growing2-TIL-VDJ

description: polyA RNA 5' capture VDJ enriched

value: Growing/Progressor


title: RNA3 - Puro1


title: RCdM0_2


title: RNA2 - ABCC1(WT)3

value: pSBbi-Hyg-APP, pSBbi-Pur-ABCC1(WT)


title: RCdM0_1


title: Growing3-Spln-5p

description: polyA RNA 5' capture GEX

value: Spleen


title: S14


title: RNA2 - ABCC1(WT)2


title: RCd0_3

value: 20 days+0 days to treated by 50 μmol/L CdCl2


title: Regressing3-Spln-5p

description: polyA RNA 5' capture GEX


title: RNA2 - ABCC1(WT)1


title: S13


title: Regressing2-Spln-5p

description: polyA RNA 5' capture GEX


title: S12

value: B


title: RNA3 - Puro3


title: S11


title: RNA2 - Puro2


title: Regressing3-TIL-5p

description: polyA RNA 5' capture GEX

value: Tumor


title: LCdM5_3

source_name: leaves

value: Italian Lettuce

value: leaves

value: 20 days+5 days to treated by 50 μmol/L CdCl2 and 1μmol/L melatonin


title: RCd0_1

value: roots


title: S9

value: BRSV challenged

value: Holstein-Friesian


title: S10

value: Fresh


title: Regressing1-TIL-VDJ

description: polyA RNA 5' capture VDJ enriched

value: (1) single-cell RNA sequencing


title: S8


title: Regressing2-TIL-5p

description: polyA RNA 5' capture GEX

value: Regressing/Regressor


title: Ln_NGF_D2

city: Taipei

first: Yen-Nien

last: Liu

state: Please Select

address: No. 250, Wu-Hsing Street

country: Taiwan

institute: Taipei Medical University

data_processing:
In the data modulation step, the quality of raw reads was checked by FastQC and MultiQC, and then raw-paired end reads were trimmed with Trimommatic v0.38 (Leading: 3; Trailing: 3; Slidingwindow: 4:15; Minlen: 30) following by DIAMOND to detect contamination.
Clean reads were mapped to the reference genome (Homo sapiens GRCh38) by HISAT2 v2.1.0. FeatureCount v1.6.0 was used to map count readings to an individual gene.
Read counts underwent relative log expression normalization by the DESeq2 v1.22.1 package in R. Parameters and codes from each R package followed the default except for those mentioned above.
Differentially expressed genes (DEGs) were determined using DESeq2 the threshold of significance of which was set to log (fold change) of > 2 and p-adjusted of < 0.05 based on Benjamini and Hochberg’s approach.
Supplementary_files_format_and_content: A Gene Ontology analysis and KEGG pathway enrichment analysis of DEGs were carried out using clusterProfiler v3.10.1. A GSEA was carried out with 1000 permutations to identify activated enriched pathways from MSigDB.

source_name: LNCaP cells with NGF cDNA expression_rep2

growth_protocol: LNCaP/EV and LNCaP/NGF cells were cultured in RPMI 1640 medium supplemented with 10% FBS.

extract_protocol:
An RNeasy Midi Kit (Qiagen, Redwood City, CA, USA) was used for total RNA isolation.
The cDNA library was prepared by KAPA mRNA HyperPrep Kits (Roche) and sequenced using the NovaSeqTM 6000 sequencing system (Illumina, San Diego, CA, USA) in 300~400-bp paired-end reads.

value: LNCaP

value: Human prostate cancer cell line

value: NGF cDNA vector


title: LCdM5_1


title: S7


title: Ln_NGF_D1

source_name: LNCaP cells with NGF cDNA expression_rep1


title: Growing1-TIL-3p

description: polyA RNA 3' capture GEX

source_name: Tumor-infiltrating cells

value: Growing/Progressor


title: RNA2 - Puro3

value: pSBbi-Hyg-APP, pSBbi-Pur


title: RCd0_2

value: 20 days+0 days to treated by 50 μmol/L CdCl2


title: S6

value: control

value: A


title: Ln_EV_N2

source_name: LNCaP cells with empty vector expression_rep2

value: empty vector


title: Regressing1-TIL-3p

description: polyA RNA 3' capture GEX

value: Tumor


title: Growing3-TIL-5p

description: polyA RNA 5' capture GEX


title: Ln_EV_N1

source_name: LNCaP cells with empty vector expression_rep1


title: S5


title: LCd5_3

value: Italian Lettuce

value: leaves

value: 20 days+5 days to treated by 50 μmol/L CdCl2


title: LCd5_2


title: LCd5_1


title: RNA2 - Puro1


title: Growing2-TIL-5p

description: polyA RNA 5' capture GEX


title: TRF2-DN-Dox_3

city: Pittsburgh

first: Jonathan

middle: K.

last: Alder

state: PA

address: 3459 Fifth Ave, NW 628

institute: University of Pittsburgh

data_processing:
Data processing was performed by Novogene. Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads. Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix file with FPKM for all samples

growth_protocol: Cells were grown understandard conditions (DMEM, 10% FBS). Cells were passaged when they became confluent

extract_protocol:
Total RNA was extracted using RNAeasy columns according to manufactor's protocol (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene

treatment_protocol: Some samples were treated with doxicycline (2 micrograms per mL)

tag: cell line background

value: A549 stable cell line

value: Doxicycline


title: S4

value: Holstein-Friesian

value: Fresh


title: LCdM5_2

value: 20 days+5 days to treated by 50 μmol/L CdCl2 and 1μmol/L melatonin


title: DLD-1 IOX1 treatment

city: Richmond

first: Jiong

last: Li

state: Virginia

address: 800 E Leigh Street, suite 212

institute: VCU

data_processing:
RNAs were single-end sequenced on Illumina machines
Reads was aligned using Tophat with the hg18 build of the human genome.
Transcript assembly and differential expression were determined using Cufflinks with Refseq mRNAs.
RNA-seq data was analyzed using the cummeRbund package in R.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

source_name: colorectal cancer cells

growth_protocol: 10% FBS in DMEM

extract_protocol:
Total RNA was isolated from cells using NucleoSpin® RNA II RNA purification kit (Machery-Nagel; #740955.20).
Sequencing libraries were generated using a KAPA RNA-Seq Library Preparation Kits (KAPA Biosystems, cat#07960140001)

treatment_protocol: cells were treated with 10 uM of IOX1 or control for 24 hours

tag: cell line

value: colorectal cancer cells


title: DLD-1 control


title: LCdM1_3

value: 20 days+1 days to treated by 50 μmol/L CdCl2 and 1μmol/L melatonin


title: TRF2-DN-Dox_2


title: LCdM1_2

value: 21 days+1 days to treated by 50 μmol/L CdCl2 and 1μmol/L melatonin


title: HCP-1 IOX1 treatment


title: TRF2-DN-Dox_1


title: S3


title: S2


title: LCdM1_1


title: HCP-1 control


title: TRF2-DN_3


title: S1


title: TRF2-DN_2


title: LCd1_3

value: 20 days+1 days to treated by 50 μmol/L CdCl2


title: HCT116 control


title: TRF2-DN_1


title: LP_SL_sRNA-seq

city: beijing

first: junhong

last: zhang

address: Xiangshan Road

institute: Chinese Academy of Forestry

data_processing:
The raw reads were subjected to the Illumina pipeline filter (Solexa 3.0), and the dataset was further processed using an in-house program (ACGT101-miR; LC Sciences, Houston, TX) to remove adaptors, junk, regions of low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats.
The filtered sequencing reads were compared to known miRNAs in miRBase 22.0  and the remaining sRNA sequences were used to identify potential novel miRNAs, based on the criteria for the miRNA definition.
Supplementary_files_format_and_content: counts

organism: Betula luminifera

source_name: shoots under LP condition

growth_protocol: The B. luminifera clone designated G49# was propagated in vitro in the laboratory at 25 ± 2°C under fluorescent light with a 16-h photoperiod, and the seedlings were grown in Murashige and Skoog (MS) medium (Murashige and Skoog,1962) without growth regulators. Two-month-old tissue culture seedlings of G49# were subsequently planted in pots with washed and sterilized sand, with three holes at the bottom of the pot for drainage. Then, seedlings grown in an incubator with a light intensity of 150 μmol/m2/s and temperature of 25°C/20°C (day/night). Modified liquid MS medium without organic compounds and sugar was used in subsequent experiment.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Total RNA quality and quantity were analyzed using a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent Technologies, Santa Clara, CA, USA) with RNA integrity number (RIN) >7.0. Under CK and LP treatment, root RNA was used to construct a root library, and equal quantities of RNA from stems and leaves were pooled to generate a shoot library.
Approximately 1 μg of total RNA was used to construct an sRNA library using a TruSeq Small RNA Sample Prep Kit in accordance with the manufacturer’s protocol (Illumina, San Diego, CA, USA). Single-end sequencing (36 bp) was then performed on an Illumina HiSeq2500 at the facilities of LC-BIO (Hangzhou, China), in accordance with the manufacturer’s recommended protocol. Four sRNA libraries designated CK_R, CK_SL, LP_R, and LP_SL were constructed.

treatment_protocol: Seedlings in sand were irrigated with modified liquid MS medium containing normal Pi for two weeks, then irrigated with deionized water for two weeks to eliminated accumlated Pi. Then, 54 uniformly developed plants were used in our subsequent experiments, which were evenly and randomly divided into two groups, and the completely randomized block design with three replicates was used. For the control (CK) treatment, we used modified liquid MS medium containing 1.25 mM KH2PO4. For phosphate deficiency treatment (LP), we used modified MS formulation without KH2PO4 (the only source of Pi), and adjusted the K+ concentration accordingly by adding K2SO4 (Jain et al. 2009; Zeng et al. 2016). The pH of the medium was adjusted to 5.7, and 20 mL of medium was used for irrigation every day to maintain a constant concentration of Pi in the sand.

value: shoots


title: LCd1_2


title: CK_SL_sRNA-seq

source_name: shoots under CK condition


title: LP_R_sRNA-seq

source_name: roots under LP condition

value: roots


title: LCd1_1


title: LCdM0_2

value: 20 days+0 days to treated by 50 μmol/L CdCl2 and 1μmol/L melatonin


title: LCdM0_3


title: A549-Dox_2

value: A549 cell line

value: WT


title: CK_R_sRNA-seq

source_name: roots under CK condition


title: A549-Dox_3


title: A549-Dox_1


title: A549_3


title: LP_R_RNA-seq

data_processing:
Paired-end sequencing was then performed on an Illumina Hiseq2500
Cutadapt (1.9 version) and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases (fqtrim 0.94).
sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/),including the Q20, Q30 and GC-content of the clean data.
De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content.
Supplementary_files_format_and_content: counts

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Total RNA quality and quantity were analyzed using a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent Technologies, Santa Clara, CA, USA) with RNA integrity number (RIN) >7.0. Under CK and LP treatment, root RNA was used to construct a root library, and equal quantities of RNA from stems and leaves were pooled to generate a shoot library.
For transcriptome sequencing, approximately 10 mg of total RNA was subjected to poly(A) mRNA isolation using poly-T oligo-attached magnetic beads (Invitrogen). Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature conditions. The cleaved RNA fragments were then reverse transcribed to generate the final cDNA library using the mRNA-Seq sample preparation kit (Illumina), and the average insert size for the paired-end libraries was 300 (±50) bp. Paired-end sequencing was then performed on an Illumina Hiseq2500 at the LC-BIO in accordance with the vendor’s recommended protocol.


title: A549_2


title: LP_SL_RNA-seq


title: LCd0_3

value: Italian Lettuce

value: 20 days+0 days to treated by 50 μmol/L CdCl2


title: CK_SL_RNA-seq


title: CK_R_RNA-seq


title: LCdM0_1

value: leaves


title: LCd0_1


title: KO_D3_M_20378RU

status: Public on Jan 12 2021

city: St. Louis

first: Jennifer

middle: Ann

last: McKenzie

state: MO

address: 425 S. Euclid

department: Orthopedics

institute: Washington University in St. Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: ulna

extract_protocol:
For stress fracture, a 5 mm section of the ulna was removed surrounding the injury site. Soft tissue was removed, the sample was flash frozen in liquid nitrogen, and stored at −80 °C until RNA extraction. The left ulna was similarly processed to serve as a control.Frozen bone samples were pulverized (Braun Mikrodismembrator), dissolved into TRIzol (Invitrogen), and stored at −80 °C. Later, the TRIzol-sample solution was thawed and processed using an RNA clean-up and concentration kit (Norgen Biotek). RNA concentration was measured (Thermo Scientific Nanodrop ONE) and quality was evaluated (Agilent Technologies Bioanalyzer 2100). Only samples with RINs >6.5, representing acceptable quality, were used in sequencing.
Ribo-Zero Gold

value: IL6 KO

value: stress fracture

value: 12 wk

tag: gender

value: Male


title: KO_D3_M_20467RU


title: KO_D3_F_20470RU

value: Female


title: KO_D3_F_20360RU


title: KO_D3_F_20473RU


title: WT_D3_M_20370RU

value: IL6 WT


title: WT_D3_M_20375RU


title: WT_D3_F_20421RU


title: A549_1


title: KO_D1_M_20411RU


title: KO_D1_M_20437RU


title: LCd0_2


title: KO_D1_F_20385RU


title: WT_D1_M_20395RU


title: KO_D1_M_20438RU


title: KO_D1_F_20381RU


title: WT_D1_F_20407RU


title: WT_D1_F_20402RU


title: WT_D1_F_20382RU


title: WT_D1_F_20393RU


title: WT_D1_M_20405RU


title: WT_D3_F_20372RU


title: KO_D0_M_20376LU

value: intact


title: KO_D3_M_20376RU


title: KO_D0_M_20404LU


title: WT_D3_M_20368RU


title: KO_D0_F_20360LU


title: WT_D3_F_20424RU


title: WT_D0_F_30372LU


title: WT_D0_M_20368LU


title: KO_D0_F_20380LU


title: HCT116 IOX1 treatment

value: colorectal cancer cells


title: KO_D0_F_20381LU


title: WT_D0_M_20395LU


title: WT_D0_M_20389LU


title: KO_D1_F_20383RU


title: wildtype 5-HT neuron #4

city: Shanghai

first: ling

last: chen

address: 1239 siping Rd

institute: Tongji university

data_processing:
Clean reads were aligned to mm9 with TopHat2. Gene expression levels were estimated by Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression levels(FPKM) were estimated by Cufflinks

source_name: 5-HT neuron in dorsal raphe

extract_protocol:
Coronal brain slices including the drosal raphe neuclei (250 μm thick) were prepared. Patch electrodes with tips of 5-10 μm diameters were pulled and advanced towards the YFP-positive 5-HT neurons in the acute brain slice. Positive pressure was applied until the tips were next to the cells. Slight negative pressure was then applied until the entire somatic compartment was aspirated into the recording pipette. Immediately, the samples (less than 0.5 μl) were ejected into lysis buffer (4.5μl) and reverse transcription was performed using a SMARTer Ultra Low RNA Kit (Clontech, Japan)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain slice

value: adult (2-3 month)

value: wildtype


title: Pten-/- 5-HT neuron #1

value: Pten-/-


title: KO_D0_M_20373LU


title: Pten-/- 5-HT neuron #3


title: FITC_8cell_embryo2_3 [Tn212]

first: Zhiqiang

last: Yan

address: No.5 Yiheyuan Road Haidian District

description: Observed FITC signal

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Trim Galore (v0.4.1) were used to remove the first 11 bases of each read. Adaptor sequences and low quality bases were also trimmed with the command ‘trim_galore --clip_R1 11 --quality 20 --phred33 --stringency 3 --gzip --length 30’. The paired-end reads were trimed as single-end reads.
Bismark (v0.18.2) were used to map the clean reads to mouse genome mm9 with single-end and non-directional module (parameters: bismark --bowtie2 --non_directional ).
After alignment, PCR duplicates were removed with the picard tools.
WCG methylation level of cytosines was estimated using comstomized scripts.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: 8-cell blastomere

extract_protocol:
After removing zona pellucida, blastomeres were washed with PBS three times. Each cell was piked into a 200ul PCR tube, and incubated in lysis buffer.
Libraries were prepared using scBS-seq protocol with slightly modification

treatment_protocol: FITC dye was injected into one blastomere of each embryo

tag: develomental stage

value: 8-cell embryo


title: FITC_8cell_embryo2_4 [Tn213]

description: Observed FITC signal


title: FITC_8cell_embryo2_7 [Tn216]


title: FITC_8cell_embryo2_6 [Tn215]


title: Pten-/- 5-HT neuron #2

tag: tissue


title: wildtype 5-HT neuron #2


title: WT_D0_F_30382LU


title: wildtype 5-HT neuron #1


title: Pten-/- 5-HT neuron #4


title: FITC_8cell_embryo2_8 [Tn217]


title: FITC_8cell_embryo2_1 [Tn210]


title: FITC_8cell_embryo2_5 [Tn214]


title: FITC_8cell_embryo1_7 [Tn209]


title: FITC_8cell_embryo2_2 [Tn211]


title: FITC_8cell_embryo1_5 [Tn207]


title: FITC_8cell_embryo1_4 [Tn206]

description: Observed FITC signal


title: FITC_8cell_embryo1_3 [Tn205]

description: Observed FITC signal


title: FITC_8cell_embryo1_1 [Tn203]

description: Observed FITC signal


title: FITC_8cell_embryo1_2 [Tn204]

description: Observed FITC signal


title: WT_D0_M_20370LU


title: wildtype 5-HT neuron #3


title: FITC_4cell_embryo3_4 [Tn190]

description: Observed FITC signal

source_name: 4-cell blastomere

value: 4-cell embryo


title: FITC_4cell_embryo3_3 [Tn189]

description: Observed FITC signal


title: FITC_4cell_embryo3_2 [Tn188]


title: FITC_4cell_embryo3_1 [Tn187]


title: FITC_4cell_embryo2_2 [Tn184]


title: FITC_4cell_embryo2_3 [Tn185]

description: Observed FITC signal


title: FITC_4cell_embryo1_4 [Tn182]

description: Observed FITC signal


title: FITC_4cell_embryo1_1 [Tn179]


title: 32cell_embryoMixed_23 [Tn276]

data_processing:
library strategy: Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)
Illumina CASAVA version 1.8 were used to the basecalling.
Trim Galore (v0.4.1) were used to remove the first 11 bases of each read. Adaptor sequences and low quality bases were also trimmed with the command ‘trim_galore --clip_R1 11 --quality 20 --phred33 --stringency 3 --gzip --length 30’. The paired-end reads were trimed as single-end reads.
Bismark (v0.18.2) were used to map the clean reads to mouse genome mm9 with single-end and non-directional module (parameters: bismark --bowtie2 --non_directional ).
After alignment, PCR duplicates were removed with the picard tools.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: 32-cell blastomere

extract_protocol:
After removing zona pellucida, blastomeres were washed with PBS three times. Each cell was piked into a 200ul PCR tube, and incubated in mild lysis buffer. After short spin, lysate supernatant was transferred to a new tube, and nucleus precipitates were used for library preparation.
GpC methylase reaction was first setup with the nucleus precipitates, followed by scBS-seq library preparation protocol with slightly modification.

value: 32-cell embryo


title: 32cell_embryoMixed_20 [Tn273]


title: 32cell_embryoMixed_21 [Tn274]


title: FITC_4cell_embryo1_2 [Tn180]


title: FITC_8cell_embryo1_6 [Tn208]


title: FITC_4cell_embryo1_3 [Tn181]

description: Observed FITC signal


title: 32cell_embryoMixed_24 [Tn277]


title: 32cell_embryoMixed_18 [Tn271]


title: 32cell_embryoMixed_25 [Tn278]


title: 32cell_embryoMixed_16 [Tn268]


title: 32cell_embryoMixed_22 [Tn275]


title: 32cell_embryoMixed_19 [Tn272]


title: 32cell_embryoMixed_17 [Tn270]


title: 32cell_embryoMixed_14 [Tn266]


title: FITC_4cell_embryo2_1 [Tn183]


title: 32cell_embryoMixed_10 [Tn262]


title: 32cell_embryoMixed_15 [Tn267]


title: 32cell_embryoMixed_11 [Tn263]


title: 32cell_embryoMixed_8 [Tn259]


title: 32cell_embryoMixed_9 [Tn260]


title: 32cell_embryoMixed_7 [Tn258]


title: 32cell_embryoMixed_12 [Tn264]


title: 32cell_embryoMixed_6 [Tn257]


title: FITC_4cell_embryo2_4 [Tn186]

description: Observed FITC signal


title: 32cell_embryoMixed_4 [Tn255]


title: 32cell_embryoMixed_2 [Tn253]


title: 32cell_embryoMixed_1 [Tn252]


title: 32cell_embryoMixed_3 [Tn254]


title: 32cell_embryo6_6 [Tn284]


title: 32cell_embryo6_8 [Tn286]


title: 32cell_embryo6_7 [Tn285]


title: 32cell_embryo6_5 [Tn283]


title: 32cell_embryo6_3 [Tn281]


title: 32cell_embryo6_2 [Tn280]


title: 32cell_embryo6_4 [Tn282]


title: 32cell_embryo5_5 [Tn251]


title: 32cell_embryo5_4 [Tn250]


title: 32cell_embryo5_2 [Tn248]


title: 32cell_embryo5_3 [Tn249]


title: 32cell_embryo4_4 [Tn245]


title: 32cell_embryo4_3 [Tn244]


title: 32cell_embryo5_1 [Tn247]


title: 32cell_embryo4_1 [Tn242]


title: 32cell_embryo3_3 [Tn167]


title: 32cell_embryo4_2 [Tn243]


title: 32cell_embryo3_4 [Tn168]


title: 32cell_embryo3_2 [Tn166]


title: 32cell_embryo2_10 [Tn163]


title: 32cell_embryoMixed_5 [Tn256]


title: 32cell_embryoMixed_13 [Tn265]


title: 32cell_embryo2_9 [Tn162]


title: 32cell_embryo3_1 [Tn164]


title: 32cell_embryo6_1 [Tn279]


title: 32cell_embryo2_8 [Tn161]


title: 32cell_embryo2_7 [Tn160]


title: 32cell_embryo2_3 [Tn156]


title: 32cell_embryo2_2 [Tn155]


title: 32cell_embryo2_4 [Tn157]


title: 32cell_embryo2_1 [Tn154]


title: 32cell_embryo1_8 [Tn153]


title: 32cell_embryo1_4 [Tn149]


title: 32cell_embryo4_5 [Tn246]


title: 32cell_embryo1_6 [Tn151]


title: 32cell_embryo1_2 [Tn147]


title: 32cell_embryo2_5 [Tn158]


title: 16cell_embryo3_7 [Tn144]

source_name: 16-cell blastomere

value: 16-cell embryo


title: 32cell_embryo1_1 [Tn146]


title: 16cell_embryo3_6 [Tn143]


title: 16cell_embryo3_4 [Tn141]


title: 16cell_embryo3_8 [Tn145]


title: 16cell_embryo3_3 [Tn140]


title: 16cell_embryo3_5 [Tn142]


title: 32cell_embryo1_5 [Tn150]


title: 16cell_embryo3_2 [Tn139]


title: 16cell_embryo2_8 [Tn137]


title: 16cell_embryo2_6 [Tn135]


title: 16cell_embryo2_7 [Tn136]


title: 16cell_embryo2_5 [Tn134]


title: 32cell_embryo2_6 [Tn159]


title: 16cell_embryo2_2 [Tn131]


title: 32cell_embryo1_7 [Tn152]


title: 16cell_embryo2_4 [Tn133]


title: 16cell_embryo2_3 [Tn132]


title: 16cell_embryo2_1 [Tn130]


title: 16cell_embryo1_8 [Tn63]


title: 16cell_embryo1_5 [Tn60]


title: 32cell_embryo1_3 [Tn148]


title: 16cell_embryo1_7 [Tn62]


title: 16cell_embryo1_6 [Tn61]


title: 16cell_embryo1_2 [Tn57]


title: 16cell_embryo1_4 [Tn59]


title: 8cell_embryo4_8 [Tn129]


title: 16cell_embryo1_1 [Tn56]


title: 8cell_embryo4_5 [Tn126]


title: 8cell_embryo4_7 [Tn128]


title: 8cell_embryo4_4 [Tn125]


title: 8cell_embryo4_3 [Tn124]


title: 8cell_embryo4_1 [Tn122]


title: 8cell_embryo3_8 [Tn121]


title: 8cell_embryo4_6 [Tn127]


title: 8cell_embryo3_7 [Tn120]


title: 8cell_embryo3_6 [Tn119]


title: 8cell_embryo3_5 [Tn118]


title: RNAseq_IMR90_sgNT_rep2

city: Stanford

first: Howard

middle: Y

last: Chang

state: California

address: 269 Campus Drive

institute: Stanford University

data_processing:
For RNA-seq, reads were mapped to the human genome (hg19) using STAR with default parameters (--outFilterMultimapNmax 1 --alignEndsType EndToEnd --outSAMattributes NH HI NM MD). Mitochodria reads were removed by samtools and duplicated reads were removed by picard. Quantification of aligned reads at the gene level was performed by HTseq count with default parameters (--stranded=reverse –additional-attr=gene_name). Raw counts were used to identify differentially expressed genes (DEG) using DESeq2 with size factor (total reads) normalization and DEGs were identified if Benjamini & Hochberg adjusted p-value <0.05.
For allelic-specific RNA-seq analysis, SNP sites for donor NA12878 were extracted from the dbSNP database. SNP sites that are shared between paternal and maternal alleles but different from the human genome were kept as the common NA12878 SNP. SNP sites that are different between paternal and maternal allele were replaced by ‘N’ to build up N-masked reference genome. To maximize the allelic read depth, two biological replicates were pooled for later analysis. RNA-seq reads were aligned to the N-masked reference genome by STAR. After alignment and removal of mitochondria reads, remaining reads were split to maternal-specific (Xa) or paternal-specific (Xi) allele using SNPsplit. Duplicated reads were removed by picard and quantification of allele-specific reads at the gene level was performed via htseq-count similar to the bulk analysis. Genes with allelic reads >10 were retained to calculate the d score (readsXi/(readsXa+readsXi)-0.5)
Genome_build: hg19
Supplementary_files_format_and_content: For RNAseq, raw read count tsv files for each sample/replicate were generated. Allele-specific raw read count tsv files were generated from samples merged with two replicates.

source_name: dCas9-Krab+ IMR90 fibroblasts transduced with non-targeting control guide RNA

growth_protocol: GM related cell lines were cultured in RPMI 1640 (Thermo Fisher Scientific) with 10% FBS (Thermo Fisher Scientific) and 1% Penicillin-Streptomycin (Gibco). IMR90 cell line were cultured in EMEM (ATCC) with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
For RNAseq, RNA was extracted in TRIzol using Quick-RNA Miniprep Kit following the manufacturer's protocol with on-column Dnase digestion (Zymo Research).
For RNAseq, at least 100ng RNA was used to prepare the RNA-seq library using TruSeq® Stranded mRNA Library Prep Kit ( Cat# 20020594, Illumina) for each sample following the manufacturer's instruction.

treatment_protocol: To inhibit DNA methylation and H3K27me3, B cell line was treated with 0.3 uM DNMT inhibitor 5-azacytidine and 2 uM EZH2 inhibitor EPZ-6438 for 7 days

value: fibroblast

tag: treatment

value: untreated

value: Non-targeting control


title: RNAseq_IMR90_sgXIST_rep2

source_name: dCas9-Krab+ IMR90 fibroblasts transduced with guide RNA targeting XIST promoter

tag: cell type

value: XIST CRISPRi perturbation


title: RNAseq_GM_Spen_deltaRRM_rep2

source_name: GM B cell line with Spen RRM deletion

value: GM B cell

tag: genotype

value: Spen RRM deletion


title: 8cell_embryo3_4 [Tn117]


title: RNAseq_GM_Trim28KO_rep1

source_name: GM B cell line with Trim28 KO

value: Trim28 KO


title: RNAseq_GM_Trim28KO_rep2


title: RNAseq_GM_Spen_deltaRRM_rep1


title: 8cell_embryo2_8 [Tn113]


title: 8cell_embryo4_2 [Tn123]


title: 8cell_embryo3_1 [Tn114]


title: 8cell_embryo2_6 [Tn111]


title: 8cell_embryo3_2 [Tn115]


title: 8cell_embryo2_5 [Tn110]


title: 8cell_embryo2_4 [Tn109]


title: 8cell_embryo2_3 [Tn108]


title: RNAseq_GM_sgXIST_ACRIIA4_rep2

source_name: dCas9-Krab+ GM B cell line stably expressed with guide RNA targeting XIST promoter, and then overexpressed with anti-CRISPR protein ACRIIA4

value: XIST CRISPRi perturbation+anti-CRISPR


title: 8cell_embryo2_2 [Tn107]


title: 8cell_embryo2_1 [Tn106]


title: RNAseq_IMR90_sgNT_rep1


title: RNAseq_GM_sgNT_ACRIIA4_rep1

source_name: dCas9-Krab+ GM B cell line stably expressed with non-targeting control guide RNA, and then overexpressed with anti-CRISPR protein ACRIIA4

value: Non-targeting control+anti-CRISPR


title: RNAseq_GM_sgNT_ACRIIA4_rep2


title: RNAseq_GM_sgXIST_inhibitors_rep2

source_name: dCas9-Krab+ GM B cell line transduced with guide RNA targeting XIST promoter

value: treated with 0.3 uM DNMT inhibitor 5-azacytidine and 2 uM EZH2 inhibitor EPZ-6438 for 7 days


title: RNAseq_GM_sgNT_inhibitors_rep2

source_name: dCas9-Krab+ GM B cell line transduced with non-targeting control guide RNA


title: RNAseq_GM_sgXIST_inhibitors_rep1


title: 8cell_embryo1_8 [Tn55]


title: 8cell_embryo1_7 [Tn54]


title: 8cell_embryo1_6 [Tn53]


title: 8cell_embryo2_7 [Tn112]


title: RNAseq_GM_sgXIST_DMSO_rep2

value: treated with DMSO for 7 days


title: RNAseq_GM_sgXIST_DMSO_rep1


title: 8cell_embryo1_4 [Tn51]


title: Cut&Run_GM_XIST_KO_IgG_rep2

data_processing:
Library strategy: Cut&Run
For ChIPseq and Cut&Run, reads were mapped to the human genome (hg19) using bowtie2 with default parameters (--very-sensitive). Mitochondrial reads were removed by samtools and duplicated reads were removed by picard. For allelic-specific analysis, to maximize the allelic read depth, two biological replicates were pooled for later analysis. Reads were aligned to the N-masked reference genome by bowtie2. After alignment and removal of mitochondria reads and duplicated reads, remaining reads were split to Xa or Xi allele using SNPsplit.
ChIP-seq or Cut&Run peaks were called using MACS2 with parameters (--broad -f BAMPE –broad-cutoff 0.01) over input control. The total consensus peak coordinate across samples was obtained using bedtools merge and intersect. The peaks were assigned to the nearest genes using HOMER annotatePeaks. The peaks within TSS +/- 1kb range were defined as promoters and other distal H3K27ac peaks were defined as enhancers. Allelic reads overlapping on peaks were counted using bedtools intersect and peaks with the allelic reads >10 were retained to calculate the d score (readsXi/(readsXa+readsXi)-0.5).
Genome_build: hg19
Supplementary_files_format_and_content: For ChIPseq and Cut&Run, bigwig files for each sample/replicate were generated. Allele-specific bigwig files were generated from samples merged with two replicates.

source_name: GM B cell line with XIST A repeat deletion

growth_protocol: GM related cell lines were cultured in RPMI 1640 (Thermo Fisher Scientific) with 10% FBS (Thermo Fisher Scientific) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
For ChIPseq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
For ChIPseq, the library was prepared using NEBNext Ultra II DNA library prep kit for Illumina (NEB) following the manufacturer's protocol

tag: antibody

value: XIST KO


title: RNAseq_GM_sgNT_DMSO_rep1


title: 8cell_embryo1_3 [Tn50]


title: 8cell_embryo1_2 [Tn49]


title: RNAseq_GM_sgXIST_ACRIIA4_rep1


title: 8cell_embryo1_1 [Tn48]


title: RNAseq_GM_sgNT_DMSO_rep2


title: Cut&Run_GM_XIST_KO_IgG_rep1


title: Late4cell_embryo6_4 [Tn241]

source_name: Late 4-cell blastomere

value: Late 4-cell embryo


title: Cut&Run_GM_XIST_WT_IgG_rep2

source_name: Wild type GM B cell line

value: wild type


title: Cut&Run_GM_XIST_WT_IgG_rep1


title: Late4cell_embryo6_3 [Tn240]


title: RNAseq_GM_sgNT_inhibitors_rep1


title: Cut&Run_GM_H3K9me3_rep2

value: H3K9me3 (Ab8898, Abcam)


title: RNAseq_IMR90_sgXIST_rep1


title: Cut&Run_GM_H3K9me3_rep1


title: Late4cell_embryo6_1 [Tn238]


title: Cut&Run_GM_XIST_WT_H3K27me3_rep2

value: H3K27me3 (Ab6002, Abcam)


title: Cut&Run_GM_XIST_KO_H3K27me3_rep1


title: Late4cell_embryo5_3 [Tn236]


title: 8cell_embryo1_5 [Tn52]

value: 8-cell embryo


title: Late4cell_embryo6_2 [Tn239]


title: Late4cell_embryo5_4 [Tn237]


title: Late4cell_embryo5_1 [Tn234]


title: Cut&Run_GM_XIST_WT_H3K27me3_rep1


title: Cut&Run_GM_XIST_KO_H3K27me3_rep2


title: Late4cell_embryo4_4 [Tn233]


title: ChIPseq_GM_XIST_WT_Input_rep1

data_processing:
For ChIPseq and Cut&Run, reads were mapped to the human genome (hg19) using bowtie2 with default parameters (--very-sensitive). Mitochondrial reads were removed by samtools and duplicated reads were removed by picard. For allelic-specific analysis, to maximize the allelic read depth, two biological replicates were pooled for later analysis. Reads were aligned to the N-masked reference genome by bowtie2. After alignment and removal of mitochondria reads and duplicated reads, remaining reads were split to Xa or Xi allele using SNPsplit.
ChIP-seq or Cut&Run peaks were called using MACS2 with parameters (--broad -f BAMPE –broad-cutoff 0.01) over input control. The total consensus peak coordinate across samples was obtained using bedtools merge and intersect. The peaks were assigned to the nearest genes using HOMER annotatePeaks. The peaks within TSS +/- 1kb range were defined as promoters and other distal H3K27ac peaks were defined as enhancers. Allelic reads overlapping on peaks were counted using bedtools intersect and peaks with the allelic reads >10 were retained to calculate the d score (readsXi/(readsXa+readsXi)-0.5).
Genome_build: hg19
Supplementary_files_format_and_content: For ChIPseq and Cut&Run, bigwig files for each sample/replicate were generated. Allele-specific bigwig files were generated from samples merged with two replicates.


title: ChIPseq_GM_XIST_KO_Input_rep1


title: Late4cell_embryo5_2 [Tn235]


title: Late4cell_embryo3_3 [Tn228]


title: Late4cell_embryo3_4 [Tn229]


title: ChIPseq_GM_XIST_WT_Input_rep2


title: Late4cell_embryo4_2 [Tn231]


title: Late4cell_embryo4_3 [Tn232]


title: ChIPseq_GM_Trim28_rep1

value: KAP1 (ab10483, Abcam)


title: Late4cell_embryo3_2 [Tn227]


title: ChIPseq_GM_XIST_KO_H3K27ac_rep2

value: H3K27ac (ab4729, Abcam)


title: Late4cell_embryo3_1 [Tn226]


title: ChIPseq_GM_XIST_KO_H3K27ac_rep1


title: Late4cell_embryo2_4 [Tn225]


title: Late4cell_embryo2_3 [Tn224]


title: ChIPseq_GM_XIST_KO_Input_rep2


title: Late4cell_embryo2_1 [Tn222]


title: ChIPseq_GM_XIST_WT_H3K27ac_rep1


title: Late4cell_embryo1_4 [Tn221]


title: Late4cell_embryo1_2 [Tn219]


title: HA738: Adult single cell RNA sequencing material

city: Montreal

first: Jack

last: Antel

state: Quebec

address: 3801 Rue University

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

data_processing:
All preprocessing steps were performed using the Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Genome_build: GRCh38
Supplementary_files_format_and_content: Log base 2 transformed gene expression. Subsetted the OL-lineage fraction via clustering followed by validation with marker genes. First column = gene names

source_name: Human brain tissue

growth_protocol: cells were sent for sequencing immediately ex-vivo

extract_protocol:
Single cells were obtained following mechanical and enzymatic (trypsin) dissociation as previously described (Cui et al. 2017) and an isotonic percoll gradient was used to remove myelin. The whole dissociated cell population was collected from the gradient (which sits between the myelin layer and the red blood cell layer), washed 3 times in PBS, and re-suspended at a concentration of 10^6 cells per ml.
Made using the GemCode Single-Cell Instrument (10x Genomics) and Single Cell 3' Library & Gel Bead Kit v2 and Chip Kit (10x Genomics)

value: brain

value: 62 years old


title: ChIPseq_GM_Trim28_rep2

value: GM B cell


title: HA776: Pediatric single cell RNA sequencing material

value: 2 years old


title: Late4cell_embryo1_1 [Tn218]


title: HA773: Pediatric single cell RNA sequencing material


title: 4cell_embryo12_4 [Tn105]

value: 4-cell embryo


title: 4cell_embryo12_3 [Tn104]


title: HFA571: Fetal single cell RNA sequencing material

value: second trimester fetal


title: HFA570: Fetal single cell RNA sequencing material


title: 4cell_embryo12_2 [Tn103]


title: HFA579: Fetal single cell RNA sequencing material


title: OPK363: Adult single cell RNA sequencing material

value: 58 years old


title: 4cell_embryo11_3 [Tn100]


title: ChIPseq_GM_XIST_WT_H3K27ac_rep2