title: Mouse_Male_Adipose_Visceral

description:
Mouse_Male_Adipose_Visceral
Mouse_FPKM_table_Mar22.xlsx

source_name: Intra-Abdominal Fat

value: Intra-Abdominal Fat


title: FC00029: Blue_4

status: Public on Dec 12 2022

type: SRA

city: Wellington

first: Sotaro

last: Ochiai

address: Gate 7 Victoria University, Keburn Parade

country: New Zealand

institute: Malaghan Institute of Medical Research

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1

library_source: transcriptomic single cell

data_processing:
Detected number of molecules for each gene per cell was counted based on molecular barcodes
Number of molecules for each gene per cell was calculated using the detection efficiency of the spike-in RNAs which were measured together with every cell (total input number of spike-in RNA molecules per cell: 39000).
Assembly: mm10 assembly from the UCSC Genome Browser using STAR ver.2.7.3a
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: C1-C8 DRG

extract_protocol:
DRGs collected from Nav1.8-Cre R26CAG-floxStop-tdTomato mice were digested using 0.5 mg/mL liberase TL, 5 mg.mL dispase II, 0.33 mg/mL papain and 0.1mg/mL Dnase I in DMEM (with 2-ME). Samples were incubated for 20 min, mechanically agitated using glass Pasteur pipettes to prepare single cell suspension. tdTomato+ cells were single cell sorted using BD FACS Aria III into tubes containing 0.4uL of 10 x SingleCellProtect and immediiately frozen in LiqN2. Cell collection and sequencing was performed at four separate occasions from 6 naive Nav1.8-Cre R26CAG-floxStop-tdTomato mice . FC00029 contains cells from 2 mice (labelled blue and red), FC00185 contains samples from 1 mouse, FC00355 from 2 mice (Control1 and Control2) and FC00404 from 1 mouse (Control6).
Library was generated as previously described (Tenno et al, 2017,  J Exp Med 214, 2933-2946. 10.1084/jem.20170729.)
scRNA-seq using digital RNA sequencing method (Shiroguchi et al. 2012, Proc Natl Acad Sci U S A 109, 1347-1352. 10.1073/pnas.1118018109.)

tag: cell type

value: Dorsal Root Ganglion

tag: tissue

value: C1-C8 DRG

tag: strain

tag: age

value: 6-12 weeks old


title: Rat_MammaryTissue_Male

city: North Chicago

first: Terry

last: Van Vleet

state: IL

address: 1 N Waukegan Rd

country: USA

institute: AbbVie

description:
Rat_MammaryTissue_Male
Rat_FPKM_table_Mar22.xlsx

library_source: transcriptomic

data_processing:
ArrayStudio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using ArrayStudio
Trimmed sequence reads were mapped to Mouse.B38, Rat.B6.0, Dog.CanFam3.1, and Macaca_fascicularis_5.0
Read count extraction and normalization were performed using ArrayStudio
Assembly: Mouse.B38, Rat.B6.0, Dog.CanFam3.1, and Macaca_fascicularis_5.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: Mammary Glands, Animal

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 200-300ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit Gold following manufacturer's protocols.

treatment_protocol:
NA
NA

value: Sprague Dawley

value: Mammary Glands, Animal

tag: Sex

value: Male

tag: treatment

value: untreated


title: FC00029: Blue_5


title: Mouse_Male_Adipose_Subcutaneous

description:
Mouse_Male_Adipose_Subcutaneous
Mouse_FPKM_table_Mar22.xlsx

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: Monkey_DorsalRootGanglia_Male_1003

description:
Monkey_DorsalRootGanglia_Male_1003
Cyno_FPKM_table_Mar22.xlsx

organism: Macaca fascicularis

source_name: Ganglia, Spinal

value: Ganglia, Spinal


title: Mouse_6_H3K27ac

city: San Francisco

first: Ilia

middle: D.

last: Vainchtein

state: California

address: 1550 4th street

department: Psychiatry

institute: UCSF

library_source: genomic

data_processing:
Reads were mapped using Bowtie2 to mouse genome (mm10).
HOMER was used to create tags and call peaks.
Peak files were merged per group and annotated with HOMER.
ATAC-seq enhancer peaks were anchored onto H3K27ac peaks.
Assembly: GRCm38, mm10
Supplementary files format and content: Excel; H3K27ac_ChIPseq_allNormTags.xlsx (normalized tags for H3K27ac-ChIPseq)
Supplementary files format and content: Excel; H3K27ac_ChIPseq_anchoredATACseq_IL33vsVehicle.xlsx (ATACseq anchored H3K27ac peaks IL33 vs Vehicle)

molecule: genomic DNA

source_name: Cortex

extract_protocol:
Microglia were isolated using a tissue homogenizer followed by 22% Percoll gradient, all on ice or 4C, and collected with FACS.
H3K27ac ChIP-seq protocol as in Nott et al., 2019.

treatment_protocol: P30 mice were unilaterally i.c.v. injected with IL-33 or vehicle and terminated after 4 hours.

value: Cortex

tag: celltype

value: Microglia

tag: antibody

value: H3K27ac (Active Motif, Cat #39685)


title: Mouse_5_input


title: Mouse_5_H3K27ac


title: Monkey_DorsalRootGanglia_Male_1002

description:
Monkey_DorsalRootGanglia_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Monkey_DorsalRootGanglia_Male_1001

description:
Monkey_DorsalRootGanglia_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_3


title: Mouse_Female_Vagina

description:
Mouse_Female_Vagina
Mouse_FPKM_table_Mar22.xlsx

source_name: Vagina

value: Vagina

value: Female


title: FC00029: Blue_2


title: Mouse_4_H3K27ac


title: Monkey_Cornea_Male_1003

description:
Monkey_Cornea_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Cornea

value: Cornea


title: FC00029: Blue_1


title: Mouse_Female_Uterus

description:
Mouse_Female_Uterus
Mouse_FPKM_table_Mar22.xlsx

source_name: Uterus

value: Uterus


title: Mouse_3_H3K27ac


title: Monkey_Cornea_Male_1002

description:
Monkey_Cornea_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_Female_Duodenum

description:
Mouse_Female_Duodenum
Mouse_FPKM_table_Mar22.xlsx

source_name: Duodenum

value: Duodenum


title: Mouse_2_input


title: Monkey_Cornea_Male_1001

description:
Monkey_Cornea_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_2_H3K27ac


title: Monkey_Colon_Male_1003

description:
Monkey_Colon_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Colon

value: Colon


title: Mouse_Female_SciaticNerve

description:
Mouse_Female_SciaticNerve
Mouse_FPKM_table_Mar22.xlsx

source_name: Sciatic Nerve

value: Sciatic Nerve


title: Mouse_Female_HarderianGland

description:
Mouse_Female_HarderianGland
Mouse_FPKM_table_Mar22.xlsx

source_name: Harderian Gland

value: Harderian Gland


title: Mouse_Female_SalivaryGland

description:
Mouse_Female_SalivaryGland
Mouse_FPKM_table_Mar22.xlsx

source_name: Salivary Glands

value: Salivary Glands


title: Mouse_1_input


title: Spleen CapQuant-seq 1

city: New York

first: Vladimir

last: Despic

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

data_processing:
Removal of low quality reads and 3'-end adapter trimming was performed with flexbar v2.5.
Removal of duplicated reads was accomplished with pyFastqDuplicateRemover.py within the pyCRAC package v1.3.2.
Read trimming was performed using seqtk package v1.3.
Read alignement to fly, mouse or human genome was conducted using Bowtie v1.2.3.
5'-end read coverage was calculated per each genomic position using BEDTools v2.28.0.
Genome_build: Drosohila melanogaster; dm6, Mus musculus; mm10, Homo sapiens; hg38.

molecule: polyA RNA

source_name: mouse organ

growth_protocol: CL57B/L wild type female mice were purchased from Charles River Laboratory, housed and maintained in standard cages with unrestricted supplies of water and food.

extract_protocol:
CapTag-seq
Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  Poly(A)+ RNA was isolated from total RNA using magnetic oligo(dT)25 beads (NEB).

tag: cell line/tissue

value: spleen

tag: genotype

value: C57BL/6 wild type

tag: purification

value: oligo(dT)25 beads


title: Heart CapQuant-seq 2

value: heart


title: Heart CapQuant-seq 1


title: Monkey_Colon_Male_1002

description:
Monkey_Colon_Male_1002
Cyno_FPKM_table_Mar22.xlsx

value: Male

value: untreated


title: Lung CapQuant-seq 2

value: lung


title: Mouse_Female_Parathyroid

description:
Mouse_Female_Parathyroid
Mouse_FPKM_table_Mar22.xlsx

source_name: Parathyroid Glands

value: Parathyroid Glands


title: Mouse_4_input [Sample4i]

data_processing:
Reads were mapped using Bowtie2 to mouse genome (mm10).
HOMER was used to create tags and call peaks.
ATAC enhancer peaks anchored onto H3K27ac signal were overlayed with FOS occupied enhancer peaks to calculate the percentage of overlap.
Overlapping peaks were annotated with HOMER.
Assembly: GRCm38, mm10
Supplementary files format and content: Excel; FOS_ChIPseq_IL33_Anchor.xlsx (ATAC enhancer peaks anchored onto H3K27ac signal were overlayed with FOS occupied enhancer peaks)

extract_protocol:
Microglia were isolated using a tissue homogenizer followed by 22% Percoll gradient, all on ice or 4C, and collected with FACS.
ChIP-seq protocol as described before for transcription factors (Texari et al., 2021)

treatment_protocol: P30 mice were unilaterally i.c.v. injected with IL-33 and terminated after 4 hours.

value: Cortex

value: Microglia


title: Lung CapQuant-seq 1


title: Monkey_CervicalSpinalCord_Male_1003

description:
Monkey_CervicalSpinalCord_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Cervical Cord

value: Cervical Cord


title: Monkey_Colon_Male_1001

description:
Monkey_Colon_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_4_FOS [Sample4c]

value: FOS (Cat# 9F6, Cell Signaling Technology)


title: Monkey_CervicalSpinalCord_Male_1002

description:
Monkey_CervicalSpinalCord_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Kindey CapQuant-seq 1

value: kidney


title: Mouse_Female_MesentericLymphNode

description:
Mouse_Female_MesentericLymphNode
Mouse_FPKM_table_Mar22.xlsx

source_name: Lymph Nodes

value: Lymph Nodes

value: Female


title: Mouse_Female_Ovary

description:
Mouse_Female_Ovary
Mouse_FPKM_table_Mar22.xlsx

source_name: Ovary

value: Ovary


title: Mouse_3_input [Sample3i]


title: Monkey_CervicalSpinalCord_Male_1001

description:
Monkey_CervicalSpinalCord_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Liver CapQuant-seq 2

value: liver


title: Mouse_Female_MammaryTissue

description:
Mouse_Female_MammaryTissue
Mouse_FPKM_table_Mar22.xlsx

source_name: Mammary Glands, Animal

value: Mammary Glands, Animal


title: Mouse_3_FOS [Sample3c]


title: Monkey_Cerebellum_Male_1003

description:
Monkey_Cerebellum_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Cerebellum

value: Cerebellum


title: Liver CapQuant-seq 1

value: C57BL/6 wild type

value: oligo(dT)25 beads


title: Mouse_Female_Liver

description:
Mouse_Female_Liver
Mouse_FPKM_table_Mar22.xlsx

source_name: Liver

value: Liver


title: Mouse_2_input [Sample2i]

source_name: Cortex


title: Mouse_1_H3K27ac

value: Male

value: H3K27ac (Active Motif, Cat #39685)


title: Brain_CapQuant-seq_2

value: brain


title: Monkey_Cerebellum_Male_1002

description:
Monkey_Cerebellum_Male_1002
Cyno_FPKM_table_Mar22.xlsx

value: untreated


title: Mouse_2_FOS [Sample2c]

value: Cortex

value: Microglia


title: Monkey_Cerebellum_Male_1001

description:
Monkey_Cerebellum_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_Female_Pancreas

description:
Mouse_Female_Pancreas
Mouse_FPKM_table_Mar22.xlsx

source_name: Pancreas

value: Pancreas


title: Mouse_Female_Kidney

description:
Mouse_Female_Kidney
Mouse_FPKM_table_Mar22.xlsx

source_name: Kidney

value: Kidney


title: Mouse_Female_Ileum

description:
Mouse_Female_Ileum
Mouse_FPKM_table_Mar22.xlsx

source_name: Ileum

value: Ileum


title: Kindey CapQuant-seq 2

value: kidney


title: Brain CapQuant-seq 1


title: Monkey_CaudateNucleus_Male_1003

description:
Monkey_CaudateNucleus_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Caudate Nucleus

value: Caudate Nucleus


title: Monkey_CaudateNucleus_Male_1002

description:
Monkey_CaudateNucleus_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: mESC CapQuant-seq 2

source_name: cell culture

growth_protocol: mES cells were maintained in Knockout DMEM supplemented with 15% heat-inactivated FBS, 100 U Penicillin-Streptomycin, 55 µM beta-mercaptoethanol, 1x MEM non-essential amino acid solution, 1,000 U ml-1LIF, 3 µM CHIR99021, and 1 µM PD0325901 at 37°C and 5% CO2.

value: mESC

value: wild type


title: mESC CapQuant-seq 1


title: Mouse_Female_Eye

description:
Mouse_Female_Eye
Mouse_FPKM_table_Mar22.xlsx

source_name: Eye

value: Eye

value: Female


title: Mouse_Female_Esophagus

description:
Mouse_Female_Esophagus
Mouse_FPKM_table_Mar22.xlsx

source_name: Esophagus

value: Esophagus


title: Monkey_CaudateNucleus_Male_1001

description:
Monkey_CaudateNucleus_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_Female_Colon

description:
Mouse_Female_Colon
Mouse_FPKM_table_Mar22.xlsx

source_name: Colon

value: Colon


title: Monkey_BuccalMucosa_Male_1003

description:
Monkey_BuccalMucosa_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Mouth Mucosa

value: Mouth Mucosa

value: Male


title: Monkey_BuccalMucosa_Male_1002

description:
Monkey_BuccalMucosa_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_6_Vehicle [ATAC-seq]

data_processing:
Reads were mapped using Bowtie2 to mouse genome (mm10).
HOMER was used to create tags and call peaks.
Peak files were merged per group and annotated with HOMER.
DESeq2 was used to identify accessible chromatin in IL-33 and Vehicle.
Motif enrichment was performed using HOMER.
Assembly: GRCm38, mm10
Supplementary files format and content: ATACseq_allNormTags.xlsx (normalized tags)

extract_protocol:
Microglia were isolated using a tissue homogenizer followed by 22% Percoll gradient, all on ice or 4C, and collected with FACS.
ATAC-seq protocol as in Buenrostro et al., 2013

tag: treatment/time point

value: 4 hours after i.c.v injection of vehicle


title: Mouse_7_Vehicle [ATAC-seq]


title: Mouse_8_Vehicle [ATAC-seq]


title: Mouse_5_Vehicle [ATAC-seq]


title: Mouse_Female_Cervix

description:
Mouse_Female_Cervix
Mouse_FPKM_table_Mar22.xlsx

source_name: Cervix Uteri

value: Cervix Uteri

value: untreated


title: Mouse_1_input [Sample1i]

value: Cortex

value: Microglia


title: Monkey_BuccalMucosa_Male_1001

description:
Monkey_BuccalMucosa_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_Female_Cecum

description:
Mouse_Female_Cecum
Mouse_FPKM_table_Mar22.xlsx

source_name: Cecum

value: Cecum


title: Mouse_4_IL33 [ATAC-seq]

value: 4 hours after i.c.v injection of IL-33


title: Mouse_1_FOS [Sample1c]

value: FOS (Cat# 9F6, Cell Signaling Technology)


title: Mouse_Female_Brain_Spinal_Cord

description:
Mouse_Female_Brain_Spinal_Cord
Mouse_FPKM_table_Mar22.xlsx

source_name: Spinal Cord

value: Spinal Cord


title: Mouse_2_IL33 [ATAC-seq]


title: Mouse_Female_Heart

description:
Mouse_Female_Heart
Mouse_FPKM_table_Mar22.xlsx

source_name: Heart

value: Heart


title: Mouse_3_IL33 [ATAC-seq]


title: Monkey_BoneMarrow_Male_1003

description:
Monkey_BoneMarrow_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Bone Marrow

value: Bone Marrow


title: Mouse_Female_Brain_Medulla

description:
Mouse_Female_Brain_Medulla
Mouse_FPKM_table_Mar22.xlsx

source_name: Medulla Oblongata

value: Medulla Oblongata


title: Monkey_BoneMarrow_Male_1002

description:
Monkey_BoneMarrow_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Monkey_BoneMarrow_Male_1001

description:
Monkey_BoneMarrow_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_1_IL33 [ATAC-seq]

value: Female


title: Monkey_Aorta_Male_1002

description:
Monkey_Aorta_Male_1002
Cyno_FPKM_table_Mar22.xlsx

source_name: Aorta

value: Aorta


title: Mouse_8_Vehicle

data_processing:
QC with FastQC (all samples passed)
Reads were aligned to mouse genome (mm10; Ensembl GRCm38) using STAR (version 2.6.0) and counted with HTSeq (version 0.9.0).
DEGs calculated using DESeq2 (version 1.24.0).
Normalized counts were generated with DESeq2 (version 1.24.0).
Assembly: GRCm38, mm10
Supplementary files format and content: excel, normalized counts for each sample
Supplementary files format and content: excel, DEGs of IL-33 vs vehicle at adjusted p<0.01

source_name: Cortex, Male

extract_protocol:
Microglia were isolated using a tissue homogenizer followed by 22% Percoll gradient, all on ice or 4C, and collected with FACS.
Nugen Ovation RNA-Seq System V2 kit

value: Cortex, Male

value: vehicle


title: Monkey_Aorta_Male_1003

description:
Monkey_Aorta_Male_1003
Cyno_FPKM_table_Mar22.xlsx

value: Male


title: Mouse_Female_Brain_FrontalCortex

description:
Mouse_Female_Brain_FrontalCortex
Mouse_FPKM_table_Mar22.xlsx

source_name: Frontal Lobe

value: Frontal Lobe


title: Mouse_Female_Adipose_Subcutaneous

description:
Mouse_Female_Adipose_Subcutaneous
Mouse_FPKM_table_Mar22.xlsx

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: Monkey_Aorta_Male_1001

description:
Monkey_Aorta_Male_1001
Cyno_FPKM_table_Mar22.xlsx

value: untreated


title: Mouse_Female_BoneMarrow

description:
Mouse_Female_BoneMarrow
Mouse_FPKM_table_Mar22.xlsx


title: Mouse_7_Vehicle


title: Monkey_AdrenalGland_Male_1003

description:
Monkey_AdrenalGland_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Adrenal Glands

value: Adrenal Glands


title: Mouse_5_Vehicle

source_name: Cortex, Female

value: Cortex, Female

value: Microglia


title: Mouse_6_Vehicle


title: Mouse_4_IL33


title: Mouse_3_IL33


title: Monkey_AdiposeFat_Male_1003

description:
Monkey_AdiposeFat_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Adipose Tissue

value: Adipose Tissue


title: LCS7711_QNZ_C_2_Clean_Data [T-Ctr-2]

first: Shan

last: Jiang

department: Taub Institute for Research on Alzheimer’s Disease and the Aging Brain

institute: Columbia University Irving Medical Center

data_processing:
Paired-end reads from fastq files were aligned and quantified with Salmon (v. 0.14.1) in default setting.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: CD8+T cells from Balb/c

growth_protocol: Mouse T cells were isolated from the spleens and lymph nodes of Balb/c, Mouse T cells and human T cells were activated with Dynabeads Mouse T-Activator CD3/CD28 (0077118, Gibco).

extract_protocol:
After 72 h coculture of T cells with DBT cells at a ratio of 4:1, T cells were collected and stained with anti-CD4 and anti-CD8 antibodies for 30 minutes at RT, then live CD8+ T cells were sorted with a FACSAria III flow cytometer (BD Biosciences). After spindown, cell pellets were frozen and shipped on dry ice to LC Sciences for total RNA extraction and total RNA NGS services.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: T cells were transfected with a lentivirus containing a control vector or an FGL2-blocking scFv vector. Cells were spun down at 1500×g for 2 h with 8 μg/mL polybrene (MilliporeSigma) in RPMI medium in a retronectin (T100B; Takara)-coated 24-well plate. T cells were used for in vivo or in vitro experiments 2 to 4 days after transfection.

value: Balb/c

value: sorted CD8+T cells

value: transfected with control vector


title: LCS7711_QNZ_treated_921_3_Clean_Data [T-anti-FGL2-3]

value: transfected with FGL2-blocking scFv


title: Monkey_AdrenalGland_Male_1002

description:
Monkey_AdrenalGland_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: LCS7711_QNZ_C_3_Clean_Data [T-Ctr-3]


title: LCS7711_QNZ_C_1_Clean_Data [T-Ctr-1]


title: Monkey_Vagina_Female_1503

description:
Monkey_Vagina_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Vagina

value: Vagina


title: Mouse_2_IL33


title: Monkey_AdrenalGland_Male_1001

description:
Monkey_AdrenalGland_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Monkey_Uvea_Female_1503

description:
Monkey_Uvea_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Uvea

value: Uvea

value: Female


title: Mouse_1_IL33


title: Monkey_Vagina_Female_1502

description:
Monkey_Vagina_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: Monkey_Uvea_Female_1502

description:
Monkey_Uvea_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: LCS7711_QNZ_treated_921_2_Clean_Data [T-anti-FGL2-2]


title: Monkey_Uvea_Female_1501

description:
Monkey_Uvea_Female_1501
Cyno_FPKM_table_Mar22.xlsx


title: HSPCs, tmTNF-ATO, scRNAseq

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

data_processing:
Fastq files were mapped using CellRanger version 6.0.1
Assembly: GRCh38
Supplementary files format and content: h5 files obtained from CellRanger

organism: Homo sapiens

source_name: umbilical cord blood

growth_protocol: HSPCs were cultured in ATO for 10 days

extract_protocol:
CD45+ cells were sorted into PBS containing 2% BSA and loaded onto a 10x Genomics chip.
library construction according to protocol for 10X Genomics Chromium Next GEM Single Cell 5' Kit v2

treatment_protocol:
For the control, organoids were supplemented with IL-7 and FLT3-L (5 ng/mL each).
For the sTNF-activated ATO, organoids were supplemented with 0.25 ng/mL of sTNF in addition to IL-7 and FLT3-L.
For the tmTNF-activated ATO, organoids were composed of 1% tmTNF-expressing stromal cells, and were supplemented with IL-7 and FLT3-L.

value: umbilical cord blood

value: hematopoietic cells

value: tmTNF-activated ATO


title: HSPCs, sTNF-ATO, scRNAseq

value: sTNF-activated ATO


title: Monkey_Uterus_Female_1503

description:
Monkey_Uterus_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Uterus

value: Uterus


title: LCS7711_QNZ_treated_921_1_Clean_Data [T-anti-FGL2-1]


title: Control2

city: Bronx

first: Hansoo

last: Song

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

description: Single Cell RNA-sequencing data from microdissected tissue of Pax2-Cre lineage containing the otic vesicle and CVG of control embryos at E10.5

data_processing:
Quality of the data was checked using FastQC v0.11.4
Sequencing reads were aligned to the mouse reference genome (mm10-2020-A) by Cell Ranger v3.1.0 (10xGenomics)
Identifyt clusters and subcluster by Seurat v 4.1.0
Generate loom file with Velocyto v 0.17.17
Identify single-cell fate maps, calculate abosrption probabilities, and didntify lineage genes by scVelo v0.2.3 and CellRank v1.5.1
Integrate Seurat objects by RISC v1.0 and identify DEGs
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Otic Vesicle + CVG

extract_protocol:
Three Pax2-Cre;Rosa26-GFPf/+ embryos for control and two Pax2-Cre;Tbx2f/f;Tbx3f/f;Rosa26-GFPf/+ at E10.5 (34s-36s) were collected in ice cold PBS with Ca2+ & Mg2+. The OV with CVG and immediate surrounding tissue (adjacent neural tube with pharyngeal cells) was dissected. Microdissected OVs were pooled in DMEM (GIBCO, Cat# 11885-084) at 4˚C followed by centrifugation at 100 x g for 5’ at 4˚C. DMEM was removed, and tissues were incubated with 0.25% Trypsin-EDTA (GIBCO, Cat# 25200-056) containing Dnase I (50U/mL) (Millipore, Cat# 260913-10MU) for 10’ at RT. FBS (heat inactivated, ATCC, Cat#30-2021) was added to terminate Dnase I activity. Cells were centrifuged in 4˚C at 300 x g for 5’, supernatant was removed, and cells were resuspended in PBS w/o Ca2+ & Mg2+ (Corning, Cat# 21-031-cv) with 10% FBS and filtered through a 100µm cell strainer. DAPI (Thermo Fisher Scientific, Cat# D3571) was added before cell sorting to remove the lysed cells. After filtering, the GFP+DAPI- cells were sorted with the BD FACS Aria II system (Becton, Dickinson and Company, Franklin Lakes, NJ). The sorted GFP positive cells were centrifuged in 4˚C at 300 x g for 5’ and resuspended in 50 µL PBS w/o Ca2+ & Mg2+ with 10% FBS.
10x Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

value: Otic Vesicle + CVG

tag: developmental stage

value: Swiss-Webster


title: Tbx2/3cKO 2

description: Single Cell RNA-sequencing data from microdissected tissue of Pax2-Cre lineage containing the otic vesicle and CVG of Tbx2/3cKO embryos at E10.5


title: Control1


title: Tbx2/3cKO 1


title: val1 val2 pkl R3

city: Guangzhou

first: Liang

last: Zhenwei

state: Guangdong

address: Xingang West Road

department: School of Life Science

country: China

institute: Sun Yat-sen University

data_processing:
Sequencing separately at Novogene, using Illumina nova-seq (Sequencing method: Hiseq-PE150).
Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 5,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings.
To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and val1 val2 pkl were included and compared using Cuffdiff (version 2.1.1) with default settings.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for WT and val1 val2 pkl

organism: Arabidopsis thaliana

source_name: Young seedlings

extract_protocol:
Total RNA was isolated from 14-day-old seedling using the HiPure Plant RNA Mini Kit C (Cat#R4151-02C) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: val1 val2 pkl

tag: develomental stage

tag: condition

value: LD (long day)

value: Seedling


title: Monkey_Vagina_Female_1501

description:
Monkey_Vagina_Female_1501
Cyno_FPKM_table_Mar22.xlsx

value: untreated


title: S2_Co-cultured_sample2

city: Pittsburgh

first: Da

last: Yang

address: 308 Salk Pavilion

institute: University of Pittsburgh

data_processing:
sgRNA read counts were first quantified by count_spacers.py for all five samples including the original library (P), two controls (C1 and C2) with different cultured periods, and two biological replicates of MEL-526 cells (S1 and S2) co-cultured with human gp100 TCR transduced CD8+ T cell for 4 hours.
A pseudocount of 1 was added to each sgRNA’s read count and normalization was done using the total read counts in the sample. The fold change for each sgRNA was obtained by dividing the normalized read count in the CD8+ T-cell co-cultured sample by the control followed by the base 2 logarithm transformation.
Using the GENCODE v19 annotation, we re-annotated Human CRISPR lncRNA Activation Pooled Library originally built on the hg19.refGene.gtf and CabiliSuppDataSet1_lincRNAs_transcripts.gtf. Each sgRNA sequence was considered as a DNA motif and HOMER ‘find’ function was used to identify the loci of the sgRNAs. The transcripts with at least two sgRNAs mapped to their promoters (-1000 b to + 100 b of TSS) were considered as targets of the sgRNAs in the re-annotated library.
Assembly: hg19
Supplementary files format and content: sgRNA_distribution_of_CRISPRa_screen, comma-separated values file include sgRNA annotation and read count in five samples.

source_name: Skin

extract_protocol:
Genomic DNA was harvested from the survived cells after the screen maintained coverage of >500 cells expressing each sgRNA used the Zymo Research Quick-DNA Midiprep plus kit (Zymo Research, #FD4075) according to the manufacturer’s protocol.
The extracted genomic DNA was used for PCR using NEBNext High Fidelity 2 X PCR Master Mix (NEB, #M0541S). The NGS primers that amplify the sgRNA library were listed in the protocol.
PCR amplified library

value: Skin

tag: cell line

value: melanocyte

tag: screen condition

value: T cell co-culture


title: Monkey_Uterus_Female_1502

description:
Monkey_Uterus_Female_1502
Cyno_FPKM_table_Mar22.xlsx

tag: tissue


title: S1_Co-cultured_sample1

tag: cell type


title: val1 val2 pkl R1


title: Monkey_UrinaryBladder_Female_1503

description:
Monkey_UrinaryBladder_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Urinary Bladder

value: Urinary Bladder


title: WT R3

value: wild type


title: Monkey_UrinaryBladder_Female_1502

description:
Monkey_UrinaryBladder_Female_1502
Cyno_FPKM_table_Mar22.xlsx

value: Female


title: C1_Control1

value: no T cell control (2 weeks)


title: C2_Control2

value: no T cell control (4 weeks)


title: Cas13_XIST_crRNA1

city: Berkeley

first: Marena

middle: Isabelle

last: Trinidad

state: CA

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

data_processing:
Reads were assessed for sequencing quality with FastQC, then adapters and low-quality bases were trimmed with CutAdapt.
Samples were aligned to the GRCh38 reference genome (GENCODE Release 39) with STAR and uniquely mapped reads were used to generate a strand-specific count matrix with FeatureCounts.
EdgeR calcNormFactors was used to normalize samples according to 7 housekeeping genes (UBC, HMBS, TBP, GAPDH, HPRT1, RPL13A, ACTB) before calculating RPKM.
Transcripts with a fold-change ≥2 relative to empty vector control were considered up- or downregulated. No statistical parameters were applied given one replicate.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Unnormalized FeatureCounts results are supplied for each sample.

growth_protocol: HEK293T cells were cultured in medium containing DMEM with high glucose, GlutaMAX supplement, sodium pyruvate, 10% FBS, 25 mM HEPES pH 7.2-7.5, 1x MEM non-essential amino acids, 1x Pen/Strep, and 0.1 mM BME at 37C with 5% CO2.

extract_protocol:
Total RNA was extracted with TRIzol Reagent for one replicate.
NEBNext Ultra II Directional RNA Library Prep Kit was used to create strand-specific cDNA from polyA-enriched mRNA.
Each sample was sequenced to an avearge depth of ~30 million reads on a NovaSeq 6000 using a 150 bp paired-end run configuration.

treatment_protocol: 1x10^6 HEK293T cells were transfected with 2.5 ug plasmid DNA using 7.5 ul FuGENE HD transfection reagent in 6-well plates, as per manufacturer’s instructions. Following transfection, cells were grown for 48 hr to allow plasmid expression and RNA knockdown to occur. Transfected cells (mCherry-positive) were enriched by FACS.

value: Female embryonic kidney

value: Cas13 XIST knockdown


title: shRNA_XIST_crRNA1

value: shRNA XIST knockdown

value: shRNA


title: Empty_Vector

value: WT

value: Control


title: Csm_Non_Targeting_crRNA


title: WT neural crest cells, scRNA-seq

city: AURORA

first: James

middle: Tucker

last: Nichols

state: CO

department: Craniofacial Biology

institute: University of Colorado - Anschutz Medical Campus

data_processing:
*Pre-processing* for the unselected strain:
make ref / make fastq files / aggr command / count command; CellRanger 2.2.0
create seurat object; Seurat v3 ;CreateSeuratObject() with min.cells = 5, min.features = 100; #e10x <- merge(x = wt, y = mut, project = "n10x")
subset and filter mitochondrial genes and cells with <250 genes per cell; Seurat v3; #e10x[["percent.mt"]] <- PercentageFeatureSet(e10x, pattern = "^mt-"), #e10x <- subset(x = e10x, subset = nFeature_RNA > 250 & percent.mt < 2.5)
Normalize data, find variable features, and scale; Seurat v3; NormalizeData() with scale.factor = 10000, FindVariableFeatures(e10x, mean.function = ExpMean, dispersion.function = LogVMR, mean.cutoff = c(0.0125, 3), dispersion.cutoff = c(0.5, Inf)), ScaleData(object = e10x, vars.to.regress = c("nCount_RNA", "percent.mt"), verbose = T)
dim reduction and clustering; Seurat v3;  RunPCA(e10x, features = e10x@assays$RNA@var.features, npcs = 100, ndims.print = 1:5, nfeatures.print = 5), FindNeighbors(e10x, dims = 1:12), FindClusters(e10x, resolution = 0.5), RunTSNE(e10x, reduction = "pca", tsne.method = "FIt-SNE", dims = 1:12), RunUMAP(e10x, reduction = "pca", dims = 1:12); FindAllMarkers(e10x, only.pos = TRUE, min.pct = 0.25, thresh.use = 0.25)
Assembly: GRCz11/danRer11

organism: Danio rerio

source_name: Neural crest cells

growth_protocol: Animals were maintained and staged according to established protocols (Westerfield, 1993, Kimmel et al., 1995).

extract_protocol:
60 double transgenic from the flia:EGFP;sox10:mRFP breeding line were dissociated into single cell suspension using cold-active protease from Bacillus licheniformis, DNase, EDTA, and trituration (Adam et al., 2017)
10X Genomics libraries

value: Neural crest cells

tag: tissue source

value: neuroectoderm

tag: strain

value: AB strain

tag: age

value: 24 hpf


title: WT R2

value: LD (long day)

value: Seedling


title: HSPCs, control-ATO, scRNAseq

value: umbilical cord blood

value: hematopoietic cells

tag: treatment

value: control ATO


title: P_Plasmid

value: Skin

value: melanocyte

value: plasmid


title: Cas13_SMARCA1_crRNA1

value: Female embryonic kidney

value: Cas13 SMARCA1 knockdown


title: shRNA_SMARCA1_crRNA1

value: shRNA SMARCA1 knockdown

value: shRNA


title: Monkey_UrinaryBladder_Female_1501

description:
Monkey_UrinaryBladder_Female_1501
Cyno_FPKM_table_Mar22.xlsx

value: Urinary Bladder

tag: Sex

value: Female

value: untreated


title: WT R1

value: wild type


title: pkl-R3

data_processing:
Sequencing separately at Novogene, using Illumina nova-seq (Sequencing method: Hiseq-PE150).
Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 5,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings.
To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for WT and pkl

value: pkl


title: Monkey_Trachea_Female_1503

description:
Monkey_Trachea_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Trachea

value: Trachea


title: Csm_SMARCA1_crRNA1

value: Csm SMARCA1 knockdown

value: Csm


title: Monkey_Uterus_Female_1501

description:
Monkey_Uterus_Female_1501
Cyno_FPKM_table_Mar22.xlsx

value: Uterus


title: val1 val2 pkl R2

value: val1 val2 pkl

value: LD (long day)

value: Seedling


title: Monkey_Trachea_Female_1502

description:
Monkey_Trachea_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: Cas13_MALAT1_crRNA2

value: Cas13 MALAT1 knockdown


title: pkl-R2


title: Csm_XIST_crRNA1

value: Female embryonic kidney

value: Csm XIST knockdown


title: shRNA_MALAT1_crRNA2

value: shRNA MALAT1 knockdown


title: Monkey_Trachea_Female_1501

description:
Monkey_Trachea_Female_1501
Cyno_FPKM_table_Mar22.xlsx


title: RPMI8402 transfected with sh-β-catenin 3

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads. Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to hg38 whole genome using bowtie2 with default parameters
htseq software was used to estimate the raw gene counts
DESeq2 R package was run to infer differentially expressed genes accross samples
Genome_build: hg38
Supplementary_files_format_and_content: txt files are generated from htseq and DESeq2 results using R

source_name: RPMI8402 T-ALL cell line

growth_protocol: Starting material was retrovirally transfected with shRNA scrambled (control) or against β-catenin. Transfected cells was selected with Hygromycin for 5 days.

extract_protocol:
Direct RNA isolation with RNeasy Mini Kit [Qiagen Ref. 74004]
Samples were processed to obtain cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina HiSeq 2000 sequencer.

value: RPMI8402 T-ALL cell line

tag: origin

value: patient-derived organoid

tag: phenotype

value: Beta-catenin knock-down

value: T-ALL cell line culture


title: RPMI8402 transfected with sh-β-catenin 2


title: pkl-R1


title: Monkey_Tongue_Female_1503

description:
Monkey_Tongue_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Tongue

value: Tongue

value: Female

value: untreated


title: RPMI8402 transfected with sh-scramble 3

value: Basal


title: WT-R2

value: wild type


title: Cas13_CKB_crRNA1

tag: genotype

value: Cas13 CKB knockdown


title: Csm_MALAT1_crRNA2

value: Csm MALAT1 knockdown

value: Csm


title: Monkey_Tongue_Female_1502

description:
Monkey_Tongue_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: WT-R3

value: LD (long day)

value: Seedling


title: WT-R1


title: Tcell_pre_expansion_GFP-negative_antigen

city: Stanford

first: Howard

middle: Y

last: Chang

address: 269 Campus Drive, CCSR 2130

department: Center for Personal Dynamic Regulomes

institute: Stanford University

description: pMHC antigen library (10x genomics 5' kit)

data_processing:
The scRNA-seq reads were aligned to GRCh38 genome and quantified using cellranger count (10x genomics). The CITE-seq reads were processed using cellranger count with antibody oligo barcode as feature reference. The TCR-seq reads were mapped to VDJ compatible reference (refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0) using cellranger vdj. pMHC antigen reads were processed either by custom scripts (for cell mixing experiment) or by cellranger count using peptide sequence as feature reference (for primary T cells)
The later analyses for single cell RNA-seq and CITE-seq were performed using SCANPY. TCR relevant analyses were performed using Scirpy
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz. TCR output files: filtered_contig_annotations.csv, clonotypes.csv

source_name: Peripheral blood

extract_protocol:
Primary T cells isolated directly from patient blood samples or peptide stimulated donor PBMC were stained with a mixture of pMHC displayed ENTER viruses. After 2 hr, cells were also stained with barcoded antibodies CD45RA, CD45RO, and IL7R (Biolegend totalseq-C, cat# 304163, cat# 304259, cat# 351356), live dead dye, CD3-APC and CD8-BV711 for 20 min on ice. Sample from each donor is also stained with unique hash-tag barcoded antibody (Biolegend totalseq-C, cat# 394661, cat# 394663). After two washes, CD8+ CD3+ GFP+ cells were sorted to load on two GEM wells of 10x genomics platform and CD8+ CD3+ GFP- cells were loaded on one GEM well, all using 5’ RNA and VDJ kits according to manufacturer’s protocol
Library was prepared using Chromium Single Cell 5ʹ RNA and VDJ kit (10x Genomics).

value: Peripheral blood

value: CD8+ T cells

tag: disease state

value: CMV seropositive

value: Freshly isolated T cells incubate with pMHC displayed VLP for 2h

tag: library type

value: pMHC antigen

tag: antibodies/tags


title: Monkey_ThyroidParathyroid_Female_1503

description:
Monkey_ThyroidParathyroid_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Thyroid Gland

value: Thyroid Gland


title: Monkey_ThyroidParathyroid_Female_1502

description:
Monkey_ThyroidParathyroid_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: tbx5 enh3, enh5, exon knockout  - diff rep 2

city: Dallas

first: Daniel

last: Armendariz

state: TX

address: 5323 Harry Hines Boulevard

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

description:
DAA340
KO_SET2: scRNA-seq

data_processing:
Provided datasets are for combined DAA339 and DAA340 scRNA-seq libraries.
scRNA-seq libraries were demultiplexed, mapped to the human reference genome (hg38), and aggregated by experiment using the Cellranger software (ver 6.0.0, 10X Genomics). Cellplex barcodes and library assignments can be found in KO_SET2_cellplex_library_assignments.csv  supplementary file. Both knockout sequencing lanes were combined using Cellranger aggr and normalized for sequencing. Cells with higher than 20% mitochondrial content were removed, as well as genes with fewer than 1 counts. The count matrix was natural log transformed and saved as a separate layer for differential gene expression calling before scaling counts to unit variance and zero mean. Clusters were defined using the Louvain algorithm. Clusters which held fewer than 1% of all cells were removed. Dataset contained in KO_SET2_SC_DF.h5ad supplementary file.
The Louvain cluster defining cardiomyocytes was isolated and re-clustered using Louvain. Clusters corresponding to cardiomyocyte gene signatures were selected and clustering above repeated to identify cardiomyocyte subpopulations. Dataset contained in KO_SET2_CM_DF.h5ad supplementary file.
Supplementary_files_format_and_content: H5AD file containing count matrix and cluster classifications for combined knockout scRNA-seq.
Supplementary_files_format_and_content: H5AD file containing count matrix and cluster classifications for cardiomyocyte subpopulations in combined knockout scRNA-seq.
Assembly: hg38

growth_protocol: H9 ESCs were maintained feeder-free in mTeSR Plus (Stemcell Tech. 100-0276) according to suggested manufacturer’s instructions on Matrigel (Corning 354277) coated plates, passaged every 3-4 days with DPBS/0.5 mM EDTA and plated in 2 uM thiazovivin (Sigma SML1045) supplemented mTeSR Plus overnight.

extract_protocol:
Library prepared following 10x v3.1 Dual Index with Cell Multiplexing protocol.
On day 8 post-differentiation, samples were washed with DPBS and dissociated to single cells with Accutase (Sigma SCR005) and resuspended in CDM3.

treatment_protocol: At 80-90% confluency, media was replaced with 3 uM CHIR99021 (Tocris 4423) supplemented CDM3 (RPMI 1640, Sigma R8758; 0.5 mg/ml human albumin, ScienCell OsrHSA; 211 ug/ml L-ascorbic acid 2-phosphate, Sigma A8960) for 48 hours followed by 2 uM Wnt-C59 (Cayman 16644) supplemented CDM3 for 48 hours with subsequent media changes every 2 days with CDM3 alone.

value: H9-derived cardiomyocytes

tag: differentiation day


title: RPMI8402 transfected with sh-scramble 1

value: RPMI8402 T-ALL cell line

value: patient-derived organoid

value: T-ALL cell line culture


title: EMP200_3

city: Shanghai

first: Yixiang

last: Xu

address: 130 Meilong Road

institute: East China University of Science and Technology

data_processing:
messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly
Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).
Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles.
After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length).
Assembly: The raw paired end reads were trimmed and quality controlled by SeqPrep  (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default  parameters. Then clean reads were separately aligned to reference genome with orientation mode  using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)[1] software. The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach[2]
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: Heart

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Heart

value: myocardial cell

value: WT

value: EMP200uM treatment and glucose deprivation for 36 h


title: EMP200_2


title: Csm_CKB_crRNA1

value: Female embryonic kidney

value: Csm CKB knockdown

value: Csm


title: RPMI8402 transfected with sh-β-catenin 1

value: Beta-catenin knock-down


title: Tcell_pre_expansion_GFP-positive_GEM-well2_antigen

value: Peripheral blood

value: CD8+ T cells


title: Monkey_ThyroidParathyroid_Female_1501

description:
Monkey_ThyroidParathyroid_Female_1501
Cyno_FPKM_table_Mar22.xlsx

data_processing:
ArrayStudio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using ArrayStudio
Trimmed sequence reads were mapped to Mouse.B38, Rat.B6.0, Dog.CanFam3.1, and Macaca_fascicularis_5.0
Read count extraction and normalization were performed using ArrayStudio
Assembly: Mouse.B38, Rat.B6.0, Dog.CanFam3.1, and Macaca_fascicularis_5.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 200-300ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit Gold following manufacturer's protocols.

value: Female

value: untreated


title: Tcell_pre_expansion_GFP-positive_GEM-well1_antigen

value: CMV seropositive

value: Freshly isolated T cells incubate with pMHC displayed VLP for 2h

value: pMHC antigen


title: Monkey_Thalamus_Female_1503

description:
Monkey_Thalamus_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Thalamus

value: Thalamus


title: CMV-TCR Jurkat T incubated with pp65 pMHC displayed VLP, rep2

data_processing:
RNA-seq reads were mapped to the human genome (hg19) using STAR with default parameters (--outFilterMultimapNmax 1 --alignEndsType EndToEnd --outSAMattributes NH HI NM MD). 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 normalization and DEGs were identified if Benjamini & Hochberg adjusted p-value<0.01 and over 2-fold change difference of gene expression
Assembly: hg19
Supplementary files format and content: tab-delimited text files include HTseq raw count for each sample

source_name: Jurkat T cell line with CMV-pp65 TCR

extract_protocol:
RNA was extracted using Quick-RNA Miniprep Kit with on-column Dnase digestion (Zymo Research).
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

value: Jurkat T cell line with CMV-pp65 TCR

value: T cells

value: incubated with pp65 displayed ENTER VLP for 2h


title: EMP200_1

value: Heart

value: myocardial cell

value: WT


title: Monkey_Tongue_Female_1501

description:
Monkey_Tongue_Female_1501
Cyno_FPKM_table_Mar22.xlsx

value: Tongue


title: RPMI8402 transfected with sh-scramble 2

value: RPMI8402 T-ALL cell line

value: patient-derived organoid

value: Basal

value: T-ALL cell line culture


title: shRNA_CKB_crRNA1

value: Female embryonic kidney

value: shRNA CKB knockdown

value: shRNA


title: EMP100_3

value: EMP100uM treatment and glucose deprivation for 36 h


title: Monkey_Thalamus_Female_1502

description:
Monkey_Thalamus_Female_1502
Cyno_FPKM_table_Mar22.xlsx

value: Female

value: untreated


title: Human_Somite_Organoids_Day5

city: Cambridge

first: Sharad

last: Ramanathan

state: MA

address: 52 Oxford St.

institute: Harvard University

description: 10x Genomics

data_processing:
Libraries were sequenced on an Illumina NovaSeq instrument using the parameters outlined in the user guide (Read1: 28 bp, i7 index: 10 bp, i5 index: 10 bp, Read2: 90 bp). After sequencing and demultiplexing, the Cell Ranger count pipeline to align reads to the GRCh38 human reference genome and produce the associated cell by gene count matrix.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Organoid

extract_protocol:
Organoids were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington Biochemical). Cells were counted on the LUNA-FX7 Automated Cell Counter (Logos Biosystems) using fluorescence detection for viability with an acridine orange/propidium iodide stain (Part No. F23011).
The sample was loaded into Chip G per the user guide from 10x Genomics, and no alterations were made at any step of the protocol (Part No. CG000315). GEMs were formed targeting 10,000 cells and reverse transcription completed immediately after. The cDNA was cleaned from the GEM reagents, amplified for a total of 11 cycles and verified via TapeStation (Agilent Technologies). Amplified cDNA was diluted and ran on the 4200 TapeStation instrument using High Sensitivity D5000 tape and reagents (Part No. 5067-5592 & 5067-5593). The amplified cDNA was fragmented, end repaired, and A-tailed followed by adaptor ligation, and PCR amplification for a total of 11 cycles with each sample receiving a unique set of dual indices (Part No. 1000215). Final libraries were diluted and ran using the High Sensitivity D5000 tape and reagents (Part No. 5067-5592 & 5067-5593) on the 4200 TapeStation (Agilent Technologies). Libraries were quantified via Kapa qPCR using the Complete Universal Kit (Part No. 07960140001, Roche Sequencing Solutions) and the CFX96 Touch Real-Time PCR Detection System (Bio-Rad Laboratories).

value: iPSC

value: Organoid

value: NCRM1 iPS cells with endogenous locus of HES7 tagged with Achilles and MESP2 tagged with mCherry


title: EMP100_1

value: Heart


title: Tcell_d10_post_expansion_GFP-negative_CITE

description: CITE-seq library (10x genomics 5' kit)

library_source: other

molecule: protein

value: Peripheral blood

value: CD8+ T cells

value: CMV seropositive

value: PBMC ex vivo peptide induced expansion for 10 days, then incubate with pMHC displayed VLP for 2h

value: ADT

value: Anti-CD45RA/TotalSeq-C0063 ; Anti-CD45RO/TotalSeq-C0087 ; Anti-CD127/TotalSeq-C0390; donor1 = Hashtag1/TotalSeq-C0251; donor2 = Hashtag2/TotalSeq-C0252


title: CMV-TCR Jurkat T incubated with pp65 pMHC tetramer, rep2

value: Jurkat T cell line with CMV-pp65 TCR

value: T cells

value: incubated with pp65 tetramer for 2h


title: Monkey_Thalamus_Female_1501

description:
Monkey_Thalamus_Female_1501
Cyno_FPKM_table_Mar22.xlsx

value: Thalamus


description:
Monkey_SubmandibularSalivaryGland_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Submandibular Gland

value: Submandibular Gland


title: GD_3

value: myocardial cell

value: WT

value: Glucose deprivation for 36 h


description:
Monkey_SubmandibularSalivaryGland_Female_1502
Cyno_FPKM_table_Mar22.xlsx

value: Female

value: untreated


description:
Monkey_SubmandibularSalivaryGland_Female_1501
Cyno_FPKM_table_Mar22.xlsx


title: GD_2

value: Heart


title: Tcell_d10_post_expansion_GFP-positive_GEM-well1_CITE

description: CITE-seq library (10x genomics 5' kit)

value: Peripheral blood


title: HeLa_RNA_siHMG20A_Rep1

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: RNA-seq

data_processing:
Paired end raw FASTQ files were quality and adaptor trimmed using trimGalore v.1.18
Alignment of the trimmed FASTQ files against the  hg19 for HeLa data was performed using hisat2 v.2.2.1 with “--min-intronlen 30 --max-intronlen 3000” parameters
Based on the BAM files and the human hg19 GTF read counts per gene for each sample were calculated using the summarizedOverlaps function of the GenomicAlignments R package
The resulting read counts were normalized using DESeq2 v.1.28.1.
DESeq2 was used for the identification of differentially expressed genes
Assembly: hg19
Supplementary files format and content: CSV of raw sequencing counts per gene

source_name: HeLa Kyoto

growth_protocol: DMEM + 10% FCS

extract_protocol:
Cells were transfected (Oligofectamine) with siRNA pools against HMG20A RNA /unspecifc control (Dharmacon). 72 hours post transfection total RNA was harvested using Rneasy mini columns with on-column Dnase digestion (QUIAGEN)
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen)

treatment_protocol: si mediated knock down of HMG20A

value: HeLa Kyoto

value: cancer cell

value: HMG20A knock down

value: siRNA pool HMG20A


title: HeLa_RNA_siHMG20A_Rep2

description: RNA-seq


title: GD_1


title: Ctrl_3

value: DMEM (high glucose, 10%FBS)


title: Tcell_d10_post_expansion_GFP-negative_TCR

description: TCR library (10x genomics 5' kit)

value: CD8+ T cells

value: CMV seropositive

value: PBMC ex vivo peptide induced expansion for 10 days, then incubate with pMHC displayed VLP for 2h

value: TCR


description:
Monkey_SubcorticalWhiteMatter_Female_1502
Cyno_FPKM_table_Mar22.xlsx

source_name: White Matter

value: White Matter


description:
Monkey_SubcorticalWhiteMatter_Female_1503
Cyno_FPKM_table_Mar22.xlsx


title: tbx5 enh3, enh5, exon knockout  - diff rep 1

description:
DAA339
KO_SET2: scRNA-seq

value: H9-derived cardiomyocytes


title: CMV-TCR Jurkat T incubated with pp65 pMHC displayed VLP, rep1

value: Jurkat T cell line with CMV-pp65 TCR

value: T cells

value: incubated with pp65 displayed ENTER VLP for 2h


title: Ctrl_2

value: myocardial cell

value: WT


title: EMP100_2

value: Heart

value: EMP100uM treatment and glucose deprivation for 36 h


title: Tcell_d10_post_expansion_GFP-positive_GEM-well1_TCR

description: TCR library (10x genomics 5' kit)

value: Peripheral blood


title: HeLa_RNA_Ctr_Rep1

description: RNA-seq

value: HeLa Kyoto

value: cancer cell

value: siRNA pool Control


description:
Monkey_SubcorticalWhiteMatter_Female_1501
Cyno_FPKM_table_Mar22.xlsx

value: Female

value: untreated


title: HeLa_GFP-HMG20A_ChIP_Rep2

description: ChIP-seq

data_processing:
Quality control of FASTQ files was done using FastQC.
Reads were aligned to a pre-compiled index of the mouse hg19 genome using Bowtie2 (default options) 2.2.9
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
For Browser visualization bigwig files with coverage information were generated using deeptools bamCoverage functio
Assembly: Genome_build: hg19
Supplementary files format and content: bigwig files (of coverage) at 25 bp resolution

extract_protocol:
Cells were crosslinked in 1% Formaldehyde and sonicated for 30 cycles using Bioruptor Nextgen (Diagenode), DNA from  input and Immunoprecipidated lysates was extracted with DNA MinElute columns (QUIAGEN)
MicroPlex Library Preparation Kit v2 (Diagenode)

treatment_protocol: stable genomic intergation of GFP-HMG20A

value: Over expression GFP-HMG20A

tag: antibody

value: anti GFP (ab290)


title: CMV-TCR Jurkat T incubated with pp65 pMHC tetramer, rep1

tag: cell line

value: incubated with pp65 tetramer for 2h


title: Tcell_d10_post_expansion_GFP-positive_GEM-well2_CITE

description: CITE-seq library (10x genomics 5' kit)

value: CD8+ T cells

value: CMV seropositive

value: PBMC ex vivo peptide induced expansion for 10 days, then incubate with pMHC displayed VLP for 2h

value: ADT

value: Anti-CD45RA/TotalSeq-C0063 ; Anti-CD45RO/TotalSeq-C0087 ; Anti-CD127/TotalSeq-C0390; donor1 = Hashtag1/TotalSeq-C0251; donor2 = Hashtag2/TotalSeq-C0252


title: Ctrl_1

value: myocardial cell

value: WT

value: DMEM (high glucose, 10%FBS)


title: Monkey_StomachPyloric_Female_1503

description:
Monkey_StomachPyloric_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Stomach

value: Stomach


title: HeLa_GFP-HMG20A_ChIP_Rep1

description: ChIP-seq

value: HeLa Kyoto


title: Tcell_d10_post_expansion_GFP-negative_GEX

description: Gene expression library (10x genomics 5' kit)

value: Peripheral blood

value: mRNA


title: Tcell_d10_post_expansion_GFP-positive_GEM-well2_GEX


title: Monkey_StomachPyloric_Female_1502

description:
Monkey_StomachPyloric_Female_1502
Cyno_FPKM_table_Mar22.xlsx

value: Female


title: HeLa_GFP_ChIP

description: ChIP-seq

value: cancer cell

value: Over expression GFP


title: HeLa_RNA_Ctr_Rep2

description: RNA-seq

value: siRNA pool Control


title: Human ESC Organoid Day 4

city: Newton

first: Giridhar

last: Anand

address: 31 Cross Street

description: 10x Genomics

data_processing:
Libraries were sequenced on an Illumina NovaSeq instrument using the parameters outlined in the user guide (Read1: 28 bp, i7 index: 10 bp, i5 index: 10 bp, Read2: 90 bp). After sequencing and demultiplexing, the Cell Ranger count pipeline was used to align reads to the GRCh38 human reference genome and produce the associated cell by gene count matrix.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Organoids differentiated for 4 days were dissociated into a single-cell suspension using the Worthington Papain Dissociation System and analyzed using scRNAseq.
The sample was loaded into Chip G per the user guide from 10x Genomics, and no alterations were made at any step of the protocol (Part No. CG000315). GEMs were formed targeting 10,000 cells and reverse transcription completed immediately after. The cDNA was cleaned from the GEM reagents, amplified for a total of 11 cycles and verified via TapeStation (Agilent Technologies). Amplified cDNA was diluted and ran on the 4200 TapeStation instrument using High Sensitivity D5000 tape and reagents (Part No. 5067-5592 & 5067-5593). The amplified cDNA was fragmented, end repaired, and A-tailed followed by adaptor ligation, and PCR amplification for a total of 11 cycles with each sample receiving a unique set of dual indices (Part No. 1000215). Final libraries were diluted and ran using the High Sensitivity D5000 tape and reagents (Part No. 5067-5592 & 5067-5593) on the 4200 TapeStation (Agilent Technologies). Libraries were quantified via Kapa qPCR using the Complete Universal Kit (Part No. 07960140001, Roche Sequencing Solutions) and the CFX96 Touch Real-Time PCR Detection System (Bio-Rad Laboratories).

value: Organoid

value: hESC


title: Tcell_d10_post_expansion_GFP-positive_GEM-well2_TCR

description: TCR library (10x genomics 5' kit)

value: CD8+ T cells

value: CMV seropositive

value: TCR


title: Monkey_StomachBody_Female_1502

first: Terry

last: Van Vleet

description:
Monkey_StomachBody_Female_1502
Cyno_FPKM_table_Mar22.xlsx

value: untreated


title: Monkey_StomachBody_Female_1503

description:
Monkey_StomachBody_Female_1503
Cyno_FPKM_table_Mar22.xlsx


title: Tcell_pre_expansion_GFP-negative_TCR

description: TCR library (10x genomics 5' kit)

value: Freshly isolated T cells incubate with pMHC displayed VLP for 2h


title: Tcell_pre_expansion_GFP-negative_CITE

description: CITE-seq library (10x genomics 5' kit)

value: ADT

value: Anti-CD45RA/TotalSeq-C0063 ; Anti-CD45RO/TotalSeq-C0087 ; Anti-CD127/TotalSeq-C0390; donor2 = Hashtag1/TotalSeq-C0251; donor1 = Hashtag2/TotalSeq-C0252


title: CMTR2 KO RNA-seq 4

description:
RNA-seq-WTandCMTR2KO-counts.xlsx
RNA-seq_differential-analysis.xlsx

data_processing:
Removal of low quality reads and 3'-end adapter trimming was performed with flexbar v2.5.
Removal of duplicated reads was accomplished with pyFastqDuplicateRemover.py within the pyCRAC package v1.3.2.
Read trimming was performed using seqtk package v1.3.
Read alignement to fly, mouse or human genome was conducted using Bowtie v1.2.3.
5'-end read coverage was calculated per each genomic position using BEDTools v2.28.0.
Genome_build: Drosohila melanogaster; dm6, Mus musculus; mm10, Homo sapiens; hg38.

source_name: cell culture

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% FBS, 100 U Penicillin-Streptomycin at 37°C and 5% CO2.

extract_protocol:
RNA-seq
Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  Poly(A)+ RNA was isolated from total RNA using magnetic oligo(dT)25 beads (NEB).

tag: cell line/tissue

value: CMTR2 knockout

tag: purification

value: Total RNA


title: Monkey_Spleen_Female_1503

description:
Monkey_Spleen_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Spleen

tag: tissue

value: Spleen


title: CMTR2 KO RNA-seq 2


title: Tcell_pre_expansion_GFP-positive_GEM-well1_CITE

description: CITE-seq library (10x genomics 5' kit)

value: Peripheral blood

tag: cell type


title: HeLa_GFP-HMG20A_input

description: ChIP-seq

value: HeLa Kyoto

value: Over expression GFP-HMG20A


title: CMTR2 KO RNA-seq 3


title: Tcell_d10_post_expansion_GFP-positive_GEM-well1_GEX

value: PBMC ex vivo peptide induced expansion for 10 days, then incubate with pMHC displayed VLP for 2h

value: mRNA


title: Monkey_StomachBody_Female_1501

description:
Monkey_StomachBody_Female_1501
Cyno_FPKM_table_Mar22.xlsx

value: Stomach

value: Female


title: Monkey_Spleen_Female_1501

description:
Monkey_Spleen_Female_1501
Cyno_FPKM_table_Mar22.xlsx


title: Tcell_pre_expansion_GFP-positive_GEM-well1_TCR

description: TCR library (10x genomics 5' kit)

value: CD8+ T cells


title: Tcell_pre_expansion_GFP-positive_GEM-well2_TCR

description: TCR library (10x genomics 5' kit)

value: CMV seropositive


title: Tcell_pre_expansion_GFP-negative_GEX


title: WT RNA-seq 4

value: wild type


title: WT RNA-seq 2


title: Monkey_Soleus_Female_1502

description:
Monkey_Soleus_Female_1502
Cyno_FPKM_table_Mar22.xlsx

source_name: Muscle, Skeletal

value: Muscle, Skeletal

value: untreated


title: Monkey_Soleus_Female_1503

description:
Monkey_Soleus_Female_1503
Cyno_FPKM_table_Mar22.xlsx


title: CMTR2 KO RNA-seq 1


title: WT RNA-seq 1


title: Tcell_pre_expansion_GFP-positive_GEM-well2_CITE

description: CITE-seq library (10x genomics 5' kit)

value: Freshly isolated T cells incubate with pMHC displayed VLP for 2h

value: ADT


title: Monkey_StomachPyloric_Female_1501

description:
Monkey_StomachPyloric_Female_1501
Cyno_FPKM_table_Mar22.xlsx


title: Tcell_pre_expansion_GFP-positive_GEM-well1_GEX


title: WT RNA-seq 3


title: Tcell_pre_expansion_GFP-positive_GEM-well2_GEX


title: Monkey_Spleen_Female_1502

description:
Monkey_Spleen_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: CMTR2 KO Polysome-TSS-seq_F5 2

description:
HEK293T-TSN-list.xlsx
CMTR2KO-MRL-rep2.xlsx

extract_protocol:
TSS-seq
Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  Poly(A)+ RNA was isolated from total RNA using magnetic oligo(dT)25 beads (NEB).

value: CMTR2 knockout

value: oligo(dT)25 beads

value: Prior to polysome extraction, cells were treated with 100 µg ml-1 cyclohexamide for 5 min.


title: CMTR2 KO Polysome-TSS-seq_F5 1

description:
HEK293T-TSN-list.xlsx
CMTR2KO-MRL-rep1.xlsx


title: Monkey_Skin_Female_1502

description:
Monkey_Skin_Female_1502
Cyno_FPKM_table_Mar22.xlsx

source_name: Skin

value: Skin


title: CMTR2 KO Polysome-TSS-seq_F4 2


title: HTPC2_FCS

city: Planegg-Martinsried

first: Artur

last: Mayerhofer

address: Großhadernerstr. 9

department: Biomedical Center

institute: LMU Munich

data_processing:
Transcriptome alignment using CellRanger 4.0.0 against the human transcriptome GRCh38.
Quality control and filtering steps: ~ 6,500 cells were selected, with at least 6,000 UMI counts, 1,600 detected genes and mitochondrial gene counts are lower than 10%.
Doublets were removed using the Scrublet framework.
Normalization and log transformation with scran.
5000 highly variable genes per group were selected using Cell Ranger flavor with fault parametrization.
SCANPY was used for cell count normalization, Scanorama for integration. Unsupervised clustering was done with the Leiden algorithm.
Cellular dynamics, differentation and related trajectories were defined with the scVelo toolkit.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: testis

extract_protocol:
HTPCs were derived from small testicular samples of two donors, with obstructive azoospermia and normal spermatogenesis, and were isolated using tissue-explant culture.
In a concentration of ~1,000 cells/µl, 10,000 cells were processed using the Single-Cell 3’ Reagent Kits v2 from 10xGenomics according to the manufacturer´s instructions. This was followed by GEM generation and barcoding, post-GEM-RT cleanup, cDNA amplification, library construction and quality assessment with the Bioanalyzer (Agilent).

value: testis

value: primary cells

value: HTPC

value: FCS


title: Monkey_SciaticNerve_Female_1503

city: North Chicago

institute: AbbVie

description:
Monkey_SciaticNerve_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Sciatic Nerve

value: Sciatic Nerve


title: Monkey_Skin_Female_1503

description:
Monkey_Skin_Female_1503
Cyno_FPKM_table_Mar22.xlsx

value: Female


title: CMTR2 KO Polysome-TSS-seq_F4 1

first: Vladimir

last: Despic


title: Monkey_Skin_Female_1501

description:
Monkey_Skin_Female_1501
Cyno_FPKM_table_Mar22.xlsx


title: Monkey_SciaticNerve_Female_1502

description:
Monkey_SciaticNerve_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: CMTR2 KO Polysome-TSS-seq_F3 1


title: HTPC2_noFCS

value: no FCS for 24 hours


title: CMTR2 KO Polysome-TSS-seq_F3 2


title: Monkey_SciaticNerve_Female_1501

description:
Monkey_SciaticNerve_Female_1501
Cyno_FPKM_table_Mar22.xlsx


title: CMTR2 KO Polysome-TSS-seq_F2 2


title: HTPC1_noFCS


title: Monkey_Retina_Female_1503

description:
Monkey_Retina_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Retina

value: Retina


title: HTPC1_FCS


title: CMTR2 KO Polysome-TSS-seq_F1 2


title: CMTR2 KO Polysome-TSS-seq_F2 1


title: Monkey_Retina_Female_1502

description:
Monkey_Retina_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: RNA-Seq-shControl-1

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

description:
sample of control of konckdown BTLA
RNAseq_knockdown_BTLA_of_A549__all_gene_RPKM.xlsx
shBTLA_vs_shControl_diff.xlsx

data_processing:
Raw reads were filtered to remove the adaptors and low-quality bases using trim_galore 0.6.6.
The filtered reads were mapped to the hg38 genome using STAR.
The counted and normalized expression of lncRNA and protein-coding transcripts were estimated using all mapped reads by featureCounts.
Differentially expressed merged transcripts were quantified using EdgeR.
Assembly: hg38
Supplementary files format and content: xls files include RPKM values for each Sample.

growth_protocol: Colonial cultures were maintained in the 1640 medium with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were sorted with directly labeled antibody of BTLA to produce 6 samples, and cells were transfected with shRNA plasmids to knockdown BTLA to produce another 6 samples

value: tumor cells

value: WT

value: knockdown control


title: RNA-Seq-shControl-2


title: RNA-Seq-shBTLA-3

description:
sample of knockdown BTLA
RNAseq_knockdown_BTLA_of_A549__all_gene_RPKM.xlsx
shBTLA_vs_shControl_diff.xlsx

value: BTLA konckdown

value: knockdown BTLA


title: Monkey_Retina_Female_1501

address: 1 N Waukegan Rd

description:
Monkey_Retina_Female_1501
Cyno_FPKM_table_Mar22.xlsx

value: untreated


title: CMTR2 KO Polysome-TSS-seq_F1 1

city: New York

institute: Weill Cornell Medicine

value: CMTR2 knockout

value: oligo(dT)25 beads


title: Monkey_Soleus_Female_1501

description:
Monkey_Soleus_Female_1501
Cyno_FPKM_table_Mar22.xlsx

value: Muscle, Skeletal


title: RNA-Seq-shControl-3


title: Cellmix_GEX

description: Gene expression library (10x genomics 5' kit)

source_name: Jurkat T cell line

value: Jurkat T cell line

value: incubate with pMHC displayed VLP for 2h

value: mRNA


title: RNA-Seq-shBTLA-2


title: Monkey_Quadriceps_Female_1503

description:
Monkey_Quadriceps_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Quadriceps Muscle

value: Quadriceps Muscle


title: WT Polysome-TSS-seq_F5 2

description:
HEK293T-TSN-list.xlsx
WT-MRL-rep2.xlsx

value: wild type

value: Prior to polysome extraction, cells were treated with 100 µg ml-1 cyclohexamide for 5 min.


title: Monkey_Quadriceps_Female_1502

description:
Monkey_Quadriceps_Female_1502
Cyno_FPKM_table_Mar22.xlsx

value: Female


title: RNA-Seq-high-3

description:
sample of cell sorting
RNAseq_low_and_high_of_A549_cell_sorting_cells_all_gene_RPKM.xlsx
low_vs_high_diff.xlsx

value: high BTLA subpopulation

value: cell sorting


title: LNCaP_DMSO_3

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

data_processing:
Sequenced reads were mapped to hg38 human genome using STAR
raw counts were calculated by STAR, RPKM/FPKM values were calculated by perl script
Genome_build: hg38
Supplementary_files_format_and_content: txt file of RPKM/FPKM values for each Sample

source_name: Human prostate cancer cells

growth_protocol: LNCaP cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin and streptomycin

extract_protocol:
Total RNA was isolated from cells using the nucleospin RNA kit (Takara) according to the manufacturer's recommended protocol.
RNA-seq libraries were prepared from 0.5 μg high-quality DNA-free total RNA by using NEBNext® Ultra RNA Library Prep Kit, according to the manufacturer’s instructions. The libraries passing quality control (equal size distribution between 250-400 bp, no adapter contamination peaks, no degradation peaks) were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603) using the Illumina provided protocol.

treatment_protocol: LNCaP cells were treated with DMSO, UNC0642 (1µM), EPZ-6438 (0.25µM) or combination of UNC0642 and EPZ-6438 for 6 days

value: LNCaP

value: prostate

tag: treatment/infection

value: DMSO

value: WT


title: LNCaP_DMSO_2


title: WT Polysome-TSS-seq_F4 2

address: 1300 York Ave

description:
HEK293T-TSN-list.xlsx
WT-MRL-rep2.xlsx


title: WT Polysome-TSS-seq_F5 1

description:
HEK293T-TSN-list.xlsx
WT-MRL-rep1.xlsx


title: RNA-Seq-high-2

value: tumor cells


title: WT Polysome-TSS-seq_F3 2

description:
HEK293T-TSN-list.xlsx
WT-MRL-rep2.xlsx


title: Monkey_Quadriceps_Female_1501

description:
Monkey_Quadriceps_Female_1501
Cyno_FPKM_table_Mar22.xlsx

value: untreated


title: LNCaP_Epz_3


title: LNCaP_DMSO_1


title: LNCaP_Epz_2


title: Monkey_Pituitary_Female_1503

description:
Monkey_Pituitary_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Pituitary Gland

value: Pituitary Gland


title: WT Polysome-TSS-seq_F4 1

description:
HEK293T-TSN-list.xlsx
WT-MRL-rep1.xlsx

value: oligo(dT)25 beads


title: RNA-Seq-high-1


title: RNA-Seq-low-3

value: low BTLA subpopulation


title: Monkey_Pituitary_Female_1501

description:
Monkey_Pituitary_Female_1501
Cyno_FPKM_table_Mar22.xlsx


title: WT Polysome-TSS-seq_F3 1

description:
HEK293T-TSN-list.xlsx
WT-MRL-rep1.xlsx


title: LNCaP_Epz_1


title: Monkey_Pituitary_Female_1502

description:
Monkey_Pituitary_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: RNA-Seq-low-2


title: LNCaP_Unc_3


title: Monkey_PeyersPatch_Female_1503

description:
Monkey_PeyersPatch_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Peyer's Patches

value: Peyer's Patches


title: WT Polysome-TSS-seq_F2 1

description:
HEK293T-TSN-list.xlsx
WT-MRL-rep1.xlsx


title: RNA-Seq-low-1


title: RNA-Seq-shBTLA-1

value: BTLA konckdown

value: knockdown BTLA


title: WT Polysome-TSS-seq_F2 2

description:
HEK293T-TSN-list.xlsx
WT-MRL-rep2.xlsx

value: wild type


title: Monkey_PeyersPatch_Female_1502

description:
Monkey_PeyersPatch_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: LNCaP_Unc_2


title: MCF-7,Input

city: Beijing

first: Zhaohan

last: Zhang

address: 10 You’anmen Outer West 1st Street

department: Biochemistry and Molecular Biology

institute: Capital Medical University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads used the fastp software, version 0.19.11, parameter setting length_ required=50; n_ base_ limit=6; poly_ x_ min_ len=10. (1) Reads with a quality value less than 15 that exceeded 40% of the number of reads for that base were removed; (2) More than 6 reads with the base n were truncated; (3) Removal of reads with adapter (adaptor); (4) Reads shorter than 50 BP after trimming were discarded;
ChIP-seq reads were aligned to the reference genome using BWA (burrows Wheeler aligner) software, version 0.7.12-r1039,.
To create ChIP-seq coverage plots, Frags were predicted using macs2 software (version 2.1.0)_ sizes.
Peaks were called uing MACS v2.1.0 with the significance cut-off p-value =0.05
Assembly: Bigwig files were generated using macs2 software (version 2.1.0)
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Breast cancer

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

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Breast cancer


title: Monkey_PeyersPatch_Female_1501

description:
Monkey_PeyersPatch_Female_1501
Cyno_FPKM_table_Mar22.xlsx

value: Female


title: MCF-7,MTA1,CST


title: WT Polysome-TSS-seq_F1 2

description:
HEK293T-TSN-list.xlsx
WT-MRL-rep2.xlsx

value: Prior to polysome extraction, cells were treated with 100 µg ml-1 cyclohexamide for 5 min.


title: Monkey_Pancreas_Female_1502

description:
Monkey_Pancreas_Female_1502
Cyno_FPKM_table_Mar22.xlsx

source_name: Pancreas

value: Pancreas


title: mESC TSS-seq

description: mESC-TSN-list.xlsx

value: mESC


title: Monkey_Pancreas_Female_1501

description:
Monkey_Pancreas_Female_1501
Cyno_FPKM_table_Mar22.xlsx


title: LNCaP_Combo_2

value: LNCaP

value: prostate

value: Combo


title: WT Polysome-TSS-seq_F1 1

description:
HEK293T-TSN-list.xlsx
WT-MRL-rep1.xlsx


title: MCF-7,CUL4B,Sigma


title: MCF-7,CXXC5,Proteintech


title: Monkey_Oviduct_Female_1503

description:
Monkey_Oviduct_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Oviducts

value: Oviducts


title: LNCaP_Combo_1

value: WT


title: MCF-7 CLAM-Cap-seq 2

growth_protocol: MCF-7 cells were maintained in DMEM supplemented with 10% FBS, 100 U Penicillin-Streptomycin at 37°C and 5% CO2.

extract_protocol:
CLAM-Cap-seq
Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  Poly(A)+ RNA was isolated from total RNA using magnetic oligo(dT)25 beads (NEB).


title: MEL526, IL10RBDT siRNA kd, RNAseq

data_processing:
Reads were aligned using STAR.
Gene expression quantification and differential expression analysis were done by cuffdiff.
Assembly: hg38
Supplementary files format and content: RNAseq_fpkm, comma-separated values file include gene expression analysis result

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen). 10 µg total RNA was treated with RNase-free DNase I (Promega) for 30 min at 37 °C and RNA cleanup was performed using the RNA Clean & Concentrator-5 columns (Zymo). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA RNA Hyper RiboErase HMR (96 rxn) following manufacturer's protocols.

value: Skin

value: melanocyte

value: IL10RB-DT siRNA knockdown


title: Monkey_Oviduct_Female_1502

description:
Monkey_Oviduct_Female_1502
Cyno_FPKM_table_Mar22.xlsx

value: untreated


title: MCF-7 CLAM-Cap-seq 1

value: oligo(dT)25 beads


title: Monkey_Pancreas_Female_1503

description:
Monkey_Pancreas_Female_1503
Cyno_FPKM_table_Mar22.xlsx


title: MCF-7 TSS-seq


title: Lapc4-b_IGO_11693_7_S9_L003_R1_001.fastq.gz

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: Human prostate cancer cells

data_processing:
To process methylation data from the epic methyl capture assay we used the BISMARK package to map the bisulfite reads to the human genome.
The Bowtie2 aligner was used in the mapping step and we used v0.23.0 of the BISMARK code.
We followed the recommended workflow as outlined in github.com/FelixKrueger/Bismark/tree/master/Docs which consisted of the following steps: genome_preparation, Bismarck mapping, deduplication and finally the quantity of the methylation signal with methylation_extractor.
Genome_build: GRCh38

growth_protocol: Cells are cultured in standard condition according to ATCC

extract_protocol:
Total genomic DNA was extracted using the Blood & Cell Culture DNA Kits (Qiagene)
Sequencing libraries were prepared using the KAPA Hyper Prep Kit (Kapa Biosystems KK8504). Post-ligation cleanup was performed using the TruSeq Methyl Capture EPIC LT Library Prep Kit (Illumina catalog # FC-151-1002).
Methyl Capture Epic sequencing

value: parental cells

tag: sample type

value: ATCC cells


title: LNCaP_Combo_3


title: VCAP-ns_IGO_11693_4_S7_L003_R1_001.fastq.gz

description: Human prostate cancer cells

source_name: VCaP


title: Monkey_Oviduct_Female_1501

description:
Monkey_Oviduct_Female_1501
Cyno_FPKM_table_Mar22.xlsx

tag: treatment


title: MCF7, nontargeting control, RNAseq

first: Da

last: Yang

source_name: Mammary gland/Breast

value: Mammary gland/Breast

value: Human epithelial cell

value: nontargeting control


title: CMTR2 KO CLAM-Cap-seq 2

source_name: cell culture

value: CMTR2 knockout


title: MEL526, LINC01198 siRNA kd, RNAseq

value: LINC01198 siRNA knockdown


title: MEL526, siCon, RNAseq

value: siRNA control


title: Monkey_Ovary_Female_1503

description:
Monkey_Ovary_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Ovary

value: Ovary

tag: Sex

value: Female


title: ABL_IGO_11693_1_S5_L003_R1_001.fastq.gz

description: Human prostate cancer cells

source_name: ABL


title: LNCaP_Unc_1

value: LNCaP

value: prostate


title: CMTR2 KO CLAM-Cap-seq 1


title: MCF7, LINC01198 activation, RNAseq

value: LINC01198 activation


title: Monkey_Ovary_Female_1502

description:
Monkey_Ovary_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: 22Rv1-b_IGO_11693_6_S6_L003_R1_001.fastq.gz

description: Human prostate cancer cells


title: mr156 shsuz12 rep3

treatment_protocol: LNCaP cells were infected with control shRNA (pLKO), shRNA targeting G9a (shG9a), shRNA targeting PALI1 (shPALI1), shRNA targeting JARID2 (shJARID2), shRNA targeting SUZ12 (shSUZ12) lentiviruses for 4-5 days.

value: WT


title: HEK293T CLAM-Cap-seq 3

value: wild type


title: Monkey_MesentericLymphNode_Female_1502

description:
Monkey_MesentericLymphNode_Female_1502
Cyno_FPKM_table_Mar22.xlsx

source_name: Lymph Nodes

value: Lymph Nodes

value: untreated


title: MEL526, LINC01198 activation, RNAseq

source_name: Skin

value: Skin

value: melanocyte


title: HEK293T CLAM-Cap-seq 2

value: oligo(dT)25 beads


title: HEK293T CLAM-Cap-seq 1


title: MEL526, nontargeting control, RNAseq


title: Monkey_MesentericLymphNode_Female_1503

description:
Monkey_MesentericLymphNode_Female_1503
Cyno_FPKM_table_Mar22.xlsx


title: mr155 shsuz12 rep2


title: Monkey_Lung_Female_1502

description:
Monkey_Lung_Female_1502
Cyno_FPKM_table_Mar22.xlsx

source_name: Lung

value: Lung


title: mr152 shJarid2 rep2


title: Monkey_Liver_Female_1503

description:
Monkey_Liver_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Liver

value: Liver


title: MEL526, IL10RBDT activation1, RNAseq

value: IL10RB-DT activation


title: MEL526, IL10RBDT activation2, RNAseq


title: CMTR2 KO ActD-TSS-seq _16 hrs 2

description:
CMTR2KO_halflife-rep2.xlsx
HEK293T-TSN-list.xlsx

data_processing:
library strategy: TSS-seq
Low quality reads were removed and the Illumina small RNA-seq 3' end adapter (DA3; 5'-TGGAATTCTCGGGTGCCAAGG-3') was trimmed off the high quality  sequencing reads using flexbar v2.5: flexbar -r sample.fastq -f i1.8 -a DA3.fasta --pre-trim-phred 30 -n 20 -s -t output --min-read-length 18. Duplicated reads were then removed using pyFastqDuplicateRemover.py script. Next, only the forawrd (R1) sequencing reads were considered for further analysis. First, a 8-nucleotide-long UMI was removed from the sequencing read 5' end, followed by read trimming to 25 bp length using seqtk. The trimmed reads were first mapped to dm6 genome build with bowtie using the following parameters: bowtie -f -v 1 -m 8 --best --strata -S -p 10 dm6.genome sample.fasta --un unmapped.fasta dm6.sam. The remaining unmapped reads were then mapped to hg38 genome build with bowtie using the following parameters: bowtie -f -v 1 -m 8 --best --strata -S -p 10 hg38.genome.index unmapped.fasta hg38.sam. Half-lives per TSN isoform were calculated by first-order decay kinetics.
Genome_build: Human: hg38; Fly: dm6
Supplementary_files_format_and_content: Text file contains measured mRNA half-lives in two independent samples from CMTR2 WT and KO cells. Additionally, the file contains differences in average half-lives between CMTR2 KO and WT samples.

extract_protocol:
Total RNA was extracted with TRIzol reagent and isopropanol precipitation. Poly(A)+ RNA was extracted using oligo(dT)25 megnetic beads.
Libraries were prepared using modified version of the TSS-seq protocol.

treatment_protocol: Cells were treated with 5 µg ml-1 actinomycin D for 16 h.

value: CMTR2 knockout

value: ActD, 16 hrs


title: CMTR2 KO ActD-TSS-seq _8 hrs 2

treatment_protocol: Cells were treated with 5 µg ml-1 actinomycin D for 8 h.

value: ActD, 8 hrs


title: mr151 shJarid2 rep1


title: mr150 shG9a rep3


title: CMTR2 KO ActD-TSS-seq _16 hrs 1

description:
CMTR2KO_halflife-rep1.xlsx
HEK293T-TSN-list.xlsx


title: iSLK.219  cells, siBANF1, 96h, Biological Replicate 2 [4BAF96]

city: Chapel Hill

first: Blossom

last: Damania

state: NC

address: 450 West Drive

department: Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

description:
96_Differential_expression_analysis_table.csv
96_GO_analysis.csv

data_processing:
Data processing was carried out by GeneWiz. Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
The gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
A gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF v.1.1-p2. The goa_human GO list was used to cluster the set of genes based on their biological processes and determine their statistical significance. A list of genes clustered based on their gene ontologies was generated.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: *_Differential_expression_analysis_table.csv: comma-delimited CSV file containing normalized hit counts for each Gene ID. Each row includes the gene  name, pvalue, adjusted pvalue, and -log10adjustedpvalue
Supplementary files format and content: *_GO_analysis.csv: comma-delimited CSV file containing significant GO terms, significant genes, significant gene count, total gene count, percent significant genes, p value, and adjusted p value

growth_protocol: iSLK.219  cells were maintained in DMEM supplemented with 10% tetracycline-free fetal bovine serum (FBS) and 1% L-glutamine in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the RNEasy Plus Mini Kit (Qiagen), flash frozen, and submitted to GeneWiz for sequencing.
2 μg of total RNA was used for library construction by GeneWiz. rRNA was removed by PolyA selection for eukaryotic mRNA. cDNA syntehsis, end repair, 5' phosphorylation, dA-tailing, adaptor ligation, and PCR enrichment were carried out by GeneWiz.

treatment_protocol: Cells were transfected with 100 nM NTC or BANF1 siRNA for 48 hours before collection of the first timepoint (48h). The media was then changed to media containing 25 ng/mL dpxycycline for 48 hours before collection of the second timepoint (96h).

value: KSHV-infected cancer cell line

value: BANF1 knockdown

value: 48h BANF1 siRNA followed by 48h doxycycline

tag: time point


title: Monkey_Liver_Female_1501

description:
Monkey_Liver_Female_1501
Cyno_FPKM_table_Mar22.xlsx

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 200-300ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit Gold following manufacturer's protocols.

value: Female


title: iSLK.219  cells, siNTC, 96h, Biological Replicate 2 [4NTC96]

value: NTC knockdown

value: 48h NTC siRNA followed by 48h doxycycline


title: Monkey_Liver_Female_1502

description:
Monkey_Liver_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: CMTR2 KO ActD-TSS-seq _8 hrs 1


title: iSLK.219  cells, siBANF1, 96h, Biological Replicate 1 [2BAF96]


title: iSLK.219  cells, siNTC, 96h, Biological Replicate 1 [2NTC96]


title: HEK293T CLAM-Cap-seq 4

value: wild type


title: mr154 shsuz12 rep1

value: LNCaP

value: prostate

value: WT


title: mr153 shJarid2 rep3


title: Monkey_MesentericLymphNode_Female_1501

description:
Monkey_MesentericLymphNode_Female_1501
Cyno_FPKM_table_Mar22.xlsx

value: Lymph Nodes

value: untreated


title: mr149 shG9a rep2


title: Monkey_LacrimalGland_Female_1503

description:
Monkey_LacrimalGland_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Lacrimal Apparatus

value: Lacrimal Apparatus


title: CMTR2 KO ActD-TSS-seq _2 hrs 2

treatment_protocol: Cells were treated with 5 µg ml-1 actinomycin D for 2 h.

value: ActD, 2 hrs

value: oligo(dT)25 beads


title: iSLK.219  cells, siBANF1, 48h, Biological Replicate 2 [4BAF48]

description:
48_Differential_expression_analysis_table.csv
48_GO_analysis.csv

value: 48h BANF1 siRNA, 0h doxycycline


title: CMTR2 KO ActD-TSS-seq _2 hrs 1

value: CMTR2 knockout


title: mr148 shG9a rep1


title: Monkey_Kidney_Female_1503

description:
Monkey_Kidney_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Kidney

value: Kidney


title: iSLK.219  cells, siBANF1, 48h, Biological Replicate 1 [2BAF48]

value: KSHV-infected cancer cell line

value: BANF1 knockdown


title: mr147 shPALI1 rep3

source_name: Human prostate cancer cells


title: iSLK.219  cells, siNTC, 48h, Biological Replicate 2 [4NTC48]

value: 48h NTC siRNA, 0h doxycycline


title: iSLK.219  cells, siNTC, 48h, Biological Replicate 1 [2NTC48]

value: NTC knockdown


title: CMTR2 KO ActD-TSS-seq _0 hrs 1

treatment_protocol: Cells were treated with 5 µg ml-1 actinomycin D for 0 h.

value: ActD, 0 hrs


title: Monkey_Kidney_Female_1501

description:
Monkey_Kidney_Female_1501
Cyno_FPKM_table_Mar22.xlsx

treatment_protocol:
NA
NA

value: Female


title: Monkey_Kidney_Female_1502

description:
Monkey_Kidney_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: CMTR2 KO ActD-TSS-seq _0 hrs 2


title: mr146 shPALI1 rep2

value: LNCaP


title: mr144 pLKO rep3

value: prostate

value: pLKO


title: WT ActD-TSS-seq _16 hrs 2

description:
WT_halflife-rep2.xlsx
HEK293T-TSN-list.xlsx

value: wild type

value: ActD, 16 hrs


title: mr143 pLKO rep2

value: WT


title: Monkey_Jejunum_Female_1502

description:
Monkey_Jejunum_Female_1502
Cyno_FPKM_table_Mar22.xlsx

source_name: Jejunum

value: Jejunum

value: untreated


title: Monkey_Jejunum_Female_1503

description:
Monkey_Jejunum_Female_1503
Cyno_FPKM_table_Mar22.xlsx


title: WT ActD-TSS-seq _16 hrs 1

description:
WT_halflife-rep1.xlsx
HEK293T-TSN-list.xlsx

value: oligo(dT)25 beads


title: Monkey_Jejunum_Female_1501

description:
Monkey_Jejunum_Female_1501
Cyno_FPKM_table_Mar22.xlsx


title: mr142 pLKO rep1


title: WT ActD-TSS-seq _8 hrs 1

value: ActD, 8 hrs


title: WT ActD-TSS-seq _2 hrs 2

value: ActD, 2 hrs


title: Monkey_Ileum_Female_1503

description:
Monkey_Ileum_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Ileum

value: Ileum


title: Monkey_Ileum_Female_1502

description:
Monkey_Ileum_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: Worm CapQuant-seq 2

organism: Caenorhabditis elegans

source_name: adult worm

growth_protocol: C. elegans was grown on the nematode growth medium (MGM) agar with OP50 E.coli strain as a food source

extract_protocol:
CapTag-seq
Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  Poly(A)+ RNA was isolated from total RNA using magnetic oligo(dT)25 beads (NEB).

value: whole


title: Worm CapQuant-seq 1


title: WT ActD-TSS-seq _2 hrs 1


title: Monkey_Ileum_Female_1501

description:
Monkey_Ileum_Female_1501
Cyno_FPKM_table_Mar22.xlsx


title: mr145 shPALI1 rep1


title: WT ActD-TSS-seq _0 hrs 2


title: Monkey_LacrimalGland_Female_1502

description:
Monkey_LacrimalGland_Female_1502
Cyno_FPKM_table_Mar22.xlsx

value: Lacrimal Apparatus


title: Monkey_Hippocampus_Female_1503

description:
Monkey_Hippocampus_Female_1503
Cyno_FPKM_table_Mar22.xlsx

source_name: Hippocampus

value: Hippocampus


title: WT ActD-TSS-seq _8 hrs 2


title: Monkey_Hippocampus_Female_1501

description:
Monkey_Hippocampus_Female_1501
Cyno_FPKM_table_Mar22.xlsx


title: Monkey_Hippocampus_Female_1502

description:
Monkey_Hippocampus_Female_1502
Cyno_FPKM_table_Mar22.xlsx


title: Monkey_Heart_Female_1502

description:
Monkey_Heart_Female_1502
Cyno_FPKM_table_Mar22.xlsx

source_name: Heart

value: Heart


title: D115

city: Jena

first: Emanuel

last: Barth

address: Leutragraben 1

department: Bioinformatics Core Facility FSU Jena

institute: Friedrich Schiller University Jena

data_processing:
RA2 adapter sequences (5’-TGGAATTCTCGGGTGCCAAGG) of the TruSeq small RNA preparation kit were clipped from all reads, using cutadapt (version 2.0), and all reads shorter than 15 bp or with a mean quality lower than 20 were removed
Mapping was performed using TopHat2 (version 2.1.1) with standard parameters onto the human reference genome (Ensembl release 98)
For counting, featureCounts (version 1.6.3) with the parameters -M, -O 0.5 was used to count reads for the mature miRNA annotations of each human pre-miRNA separately.
Assembly: GRCh38 (Ensembl release 98)
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: placenta

extract_protocol:
Total RNA was isolated using a mirVana™ miRNA Isolation Kit (cat. No. AM1561; Invitrogen), according to the manufacturer’s protocol. Approximately 100 mg placenta tissue per sample was transferred to a Medicon disposable for biological sample disaggregation (cat. No. 340591; BD Biosciences, Franklin Lakes NJ, USA) containing 1 ml of lysis buffer (provided in the kit) and processed in a Medimachine (Dako; Jena, Germany) for 20 s.
The small RNA libraries were created using Illumina’s small RNA sample preparation protocol (TruSeq Small RNA Sample Prep Kits; Illumina, San Diego, CA, USA)

treatment_protocol: Tissue samples (≤ 0.5 cm in any single dimension) were taken from central areas of control placentas and adherent tissue in PAS samples. Samples were collected immediately after delivery and washed with isotonic saline solution to remove excess blood. For RNA analysis, samples were placed in 5 mL of RNA later (cat. No. AM7021; Invitrogen Life Technologies, Darmstadt, Germany) overnight and then stored in cryotubes at -80 °C until RNA extraction.

value: placenta

tag: condition

value: Placenta Accreta Spectrum samples (PA)


title: Myeloid cells from MDA-MB-231 tumor bearing humanized mice, hashtag library

city: Bar Harbor

first: Guangwen

last: Ren

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Hashtag-derived oligonucleotide (HTO)

data_processing:
The raw data (FASTQ file) of each library were produced and demultiplexed using Illumina bcl2fastq 2.20.0.422.
For all libraries, R1 contains a 16bp cell barcode + 12bp UMI barcode and R2 contains the biological reads. If present, I1 and I2 contains the index which is needed for 10X CellRanger pipelines.
An unfiltered digital gene expression matrix was generated for each gene expression library against the 10X Genomics reference genome (GRCh38-2020-A) build using CellRanger v6.1.1
A digital counts matrix was generated for each hashtag library using CITE-Seq-Count. This produces a matrix of counts with hashtag labels for rows and cell barcodes for columns.
Assembly: GRCh38-2020-A
Supplementary files format and content: Transcriptomic and HashTag (HTO) counts matrices in Matrix Market sparse CSC matrix format. Rows correspond to genes in the order provided in features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.

organism:
Homo sapiens
Mus musculus

source_name: BM, PB, Lung, Tumor

extract_protocol:
Human CD33+ myeloid cells  were sorted from different tissues of humanized mice, and then labeled with cell hashing antibodies. Cells were loaded into one lane of a 10X Chromium microfluidic chip. Cells capture, lysis and RNA extraction were performed using the 10X V3 Chromium technology following the manufacturer’s protocol.
Single cell capture, barcoding and library preparation were performed with the 10x Chromium system using version 3 chemistry, following the manufacturer’s protocol. cDNA was synthesized and amplified as per manufacturer’s protocol and amplified to construct an Illumina sequencing library. cDNA and libraries were checked for quality on an Agilent 4200 TapeStation, quantified by KAPA qPCR.

value: BM, PB, Lung, Tumor

value: Female

value: Human CD33+ myeloid cells

tag: genotype

value: Homozygous

tag: strain


title: D123


title: Myeloid cells from MDA-MB-231 tumor bearing humanized mice, gene expression library

description: polyA RNA


title: D114


title: D100

value: control placentas (NP)


title: D75


title: Monkey_Heart_Female_1501

description:
Monkey_Heart_Female_1501
Cyno_FPKM_table_Mar22.xlsx

data_processing:
ArrayStudio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using ArrayStudio
Trimmed sequence reads were mapped to Mouse.B38, Rat.B6.0, Dog.CanFam3.1, and Macaca_fascicularis_5.0
Read count extraction and normalization were performed using ArrayStudio
Assembly: Mouse.B38, Rat.B6.0, Dog.CanFam3.1, and Macaca_fascicularis_5.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample


title: D95


title: D122


title: Myeloid cells from naïve humanized mice, gene expression library

description: polyA RNA

source_name: BM, PB, Lung

value: BM, PB, Lung


title: MCF-7 CapQuant-seq 2

source_name: cell culture

value: wild type