title: Stage E6.5 embryo 1 section 8 region EP (E6.5_Ref_8EP)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
8EP
E6.5_Ref_8EP


title: Stage E6.5 embryo 1 section 8 region EA (E6.5_Ref_8EA)

status: Public on Aug 08 2019

type: SRA

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

country: China

institute: Chinese Academy of Sciences

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
8EA
E6.5_Ref_8EA

library_source: transcriptomic

data_processing:
The reads for all samples are mapped to the mm10 using Tophat v2.0.8b with parameter: -p 20 -g 1 -N 4 --read-edit-dist 4 --microexon-search
The mapped reads were used to estimate transcriptomic alignment rates, and were also used as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each embryo

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic cells

growth_protocol: Embryos from pre-gastrulation to late-gastrulation mouse were embedded with OCT and subjected to cryosection.

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

treatment_protocol: Sample from sections were laser-microdissected and collected for single-cell based RNA sequencing.

tag: developmental stage

value: Early-gastrulation embryo (E6.5)

tag: strain

tag: cell type

value: Mouse embryonic cells

tag: section/region

value: section 8 region EA


title: Stage E6.5 embryo 1 section 7 region EP (E6.5_Ref_7EP)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
7EP
E6.5_Ref_7EP

value: section 7 region EP


title: Stage E6.5 embryo 1 section 7 region P (E6.5_Ref_7P)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
7P
E6.5_Ref_7P

value: section 7 region P


title: Stage E6.5 embryo 1 section 7 region EA (E6.5_Ref_7EA)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
7EA
E6.5_Ref_7EA

value: section 7 region EA


title: Stage E6.5 embryo 1 section 6 region P (E6.5_Ref_6P)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
6P
E6.5_Ref_6P

value: section 6 region P


title: Stage E6.5 embryo 1 section 7 region A (E6.5_Ref_7A)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
7A
E6.5_Ref_7A

value: section 7 region A


title: Stage E6.5 embryo 2 section 3 region EA (E6.5_2_3EA)

description:
E6.5_Embryo2_all.samples.genes.fpkm.txt
3EA
E6.5_2_3EA

value: section 3 region EA


title: Stage E6.5 embryo 1 section 6 region EP (E6.5_Ref_6EP)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
6EP
E6.5_Ref_6EP

value: section 6 region EP


title: Stage E6.5 embryo 1 section 6 region EA (E6.5_Ref_6EA)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
6EA
E6.5_Ref_6EA

value: section 6 region EA


title: Stage E6.5 embryo 1 section 5 region EP (E6.5_Ref_5EP)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
5EP
E6.5_Ref_5EP

value: section 5 region EP


title: Stage E6.5 embryo 1 section 5 region P (E6.5_Ref_5P)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
5P
E6.5_Ref_5P

value: section 5 region P


title: Stage E6.5 embryo 1 section 6 region A (E6.5_Ref_6A)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
6A
E6.5_Ref_6A

value: section 6 region A


title: Stage E6.5 embryo 2 section 2 region EA (E6.5_2_2EA)

description:
E6.5_Embryo2_all.samples.genes.fpkm.txt
2EA
E6.5_2_2EA

value: section 2 region EA


title: Stage E6.5 embryo 2 section 4 region A (E6.5_2_4A)

description:
E6.5_Embryo2_all.samples.genes.fpkm.txt
4A
E6.5_2_4A

value: section 4 region A


title: Stage E6.5 embryo 1 section 4 region EP (E6.5_Ref_4EP)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
4EP
E6.5_Ref_4EP

value: section 4 region EP


title: Stage E6.5 embryo 1 section 4 region A (E6.5_Ref_4A)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
4A
E6.5_Ref_4A

value: Early-gastrulation embryo (E6.5)


title: Stage E6.5 embryo 1 section 5 region A (E6.5_Ref_5A)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
5A
E6.5_Ref_5A

value: Mouse embryonic cells

value: section 5 region A


title: Stage E6.5 embryo 1 section 3 region A (E6.5_Ref_3A)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
3A
E6.5_Ref_3A

value: section 3 region A


title: Stage E6.5 embryo 1 section 3 region P (E6.5_Ref_3P)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
3P
E6.5_Ref_3P

value: section 3 region P


title: Stage E6.5 embryo 1 section 2 region EA (E6.5_Ref_2EA)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
2EA
E6.5_Ref_2EA


title: Stage E6.5 embryo 1 section 8 region A (E6.5_Ref_8A)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
8A
E6.5_Ref_8A

value: section 8 region A


title: Stage E6.5 embryo 1 section 2 region A (E6.5_Ref_2A)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
2A
E6.5_Ref_2A

value: section 2 region A


title: Stage E6.5 embryo 1 section 3 region EA (E6.5_Ref_3EA)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
3EA
E6.5_Ref_3EA


title: Stage E6.5 embryo 1 section 2 region EP (E6.5_Ref_2EP)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
2EP
E6.5_Ref_2EP

value: section 2 region EP


title: Stage E6.5 embryo 1 section 1 region EAP (E6.5_Ref_1EAP)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
1EAP
E6.5_Ref_1EAP

value: section 1 region EAP


title: Stage E6.5 embryo 1 section 4 region P (E6.5_Ref_4P)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
4P
E6.5_Ref_4P

value: section 4 region P


title: Stage E6.5 embryo 1 section 4 region EA (E6.5_Ref_4EA)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
4EA
E6.5_Ref_4EA

value: section 4 region EA


title: Stage E6.5 embryo 1 section 1 region AP (E6.5_Ref_1AP)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
1AP
E6.5_Ref_1AP

value: section 1 region AP


title: Stage E6.0 embryo 2 section 5 region VE (E6.0_Ref_5VE)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
5VE
E6.0_Ref_5VE

value: Pre-gastrulation embryo (E6.0)

value: section 5 region VE


title: Stage E6.5 embryo 1 section 2 region P (E6.5_Ref_2P)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
2P
E6.5_Ref_2P

value: section 2 region P


title: Stage E6.0 embryo 2 section 4 region P (E6.0_Ref_4B)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
4P
E6.0_Ref_4B


title: Stage E6.0 embryo 2 section 5 region A (E6.0_Ref_5A)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
5A
E6.0_Ref_5A


title: Stage E6.0 embryo 2 section 5 region P (E6.0_Ref_5B)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
5P
E6.0_Ref_5B

value: section 5 region P


title: Stage E6.0 embryo 2 section 4 region VE (E6.0_Ref_4VE)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
4VE
E6.0_Ref_4VE

value: section 4 region VE


title: Stage E6.0 embryo 2 section 4 region A (E6.0_Ref_4A)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
4A
E6.0_Ref_4A

value: section 4 region A


title: Stage E6.5 embryo 1 section 5 region EA (E6.5_Ref_5EA)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
5EA
E6.5_Ref_5EA

value: Early-gastrulation embryo (E6.5)

value: Mouse embryonic cells

value: section 5 region EA


title: Stage E6.0 embryo 2 section 3 region VE (E6.0_Ref_3VE)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
3VE
E6.0_Ref_3VE

value: section 3 region VE


title: Stage E6.5 embryo 1 section 3 region EP (E6.5_Ref_3EP)

description:
E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
3EP
E6.5_Ref_3EP

value: section 3 region EP


title: Stage E6.0 embryo 2 section 2 region VE (E6.0_Ref_2VE)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
2VE
E6.0_Ref_2VE

value: section 2 region VE


title: Stage E6.0 embryo 2 section 3 region P (E6.0_Ref_3B)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
3P
E6.0_Ref_3B

value: section 3 region P


title: Stage E6.0 embryo 2 section 1 region VE (E6.0_Ref_1VE)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
1VE
E6.0_Ref_1VE

value: section 1 region VE


title: Stage E6.0 embryo 2 section 2 region A (E6.0_Ref_2A)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
2A
E6.0_Ref_2A

value: section 2 region A


title: Stage E6.0 embryo 2 section 1 region AP (E6.0_Ref_1AP)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
1AP
E6.0_Ref_1AP


title: Stage E6.0 embryo 1 section 4 region P (E6.0_1_4B)

description:
E6.0_Embryo1_all.samples.genes.fpkm.txt
4P
E6.0_1_4B

value: section 4 region P


title: Stage E6.0 embryo 1 section 4 region A (E6.0_1_4A)

description:
E6.0_Embryo1_all.samples.genes.fpkm.txt
4A
E6.0_1_4A


title: Stage E6.0 embryo 1 section 3 region P (E6.0_1_3B)

description:
E6.0_Embryo1_all.samples.genes.fpkm.txt
3P
E6.0_1_3B


title: Stage E6.0 embryo 1 section 5 region A (E6.0_1_5A)

description:
E6.0_Embryo1_all.samples.genes.fpkm.txt
5A
E6.0_1_5A

value: section 5 region A


title: Stage E6.0 embryo 1 section 5 region P (E6.0_1_5B)

description:
E6.0_Embryo1_all.samples.genes.fpkm.txt
5P
E6.0_1_5B

value: Pre-gastrulation embryo (E6.0)


title: Stage E6.0 embryo 1 section 3 region A (E6.0_1_3A)

description:
E6.0_Embryo1_all.samples.genes.fpkm.txt
3A
E6.0_1_3A

value: section 3 region A


title: Stage E6.0 embryo 1 section 2 region P (E6.0_1_2B)

description:
E6.0_Embryo1_all.samples.genes.fpkm.txt
2P
E6.0_1_2B

value: section 2 region P


title: Stage E6.0 embryo 1 section 2 region A (E6.0_1_2A)

description:
E6.0_Embryo1_all.samples.genes.fpkm.txt
2A
E6.0_1_2A


title: Stage E6.0 embryo 1 section 1 region A/P (E6.0_1_1)

description:
E6.0_Embryo1_all.samples.genes.fpkm.txt
1AP
E6.0_1_1

value: section 1 region AP


title: Stage E5.5 embryo 2 section 5 region VE (E5.5_Ref_5VE)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
5VE
E5.5_Ref_5VE

value: Pre-gastrulation embryo (E5.5)

value: section 5 region VE


title: Stage E5.5 embryo 2 section 6 region VE (E5.5_Ref_6VE)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
6VE
E5.5_Ref_6VE

value: section 6 region VE


title: Stage E5.5 embryo 2 section 5 region A (E5.5_Ref_5A)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
5A
E5.5_Ref_5A

value: Mouse embryonic cells


title: Stage E5.5 embryo 2 section 5 region P (E5.5_Ref_5P)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
5P
E5.5_Ref_5P

value: section 5 region P


title: Stage E5.5 embryo 2 section 4 region VE (E5.5_Ref_4VE)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
4VE
E5.5_Ref_4VE

value: section 4 region VE


title: Stage E6.0 embryo 2 section 3 region A (E6.0_Ref_3A)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
3A
E6.0_Ref_3A


title: Stage E5.5 embryo 2 section 4 region P (E5.5_Ref_4P)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
4P
E5.5_Ref_4P


title: Stage E5.5 embryo 2 section 3 region VE (E5.5_Ref_3VE)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
3VE
E5.5_Ref_3VE

value: section 3 region VE


title: Stage E5.5 embryo 2 section 3 region P (E5.5_Ref_3P)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
3P
E5.5_Ref_3P


title: Stage E5.5 embryo 2 section 2 region VE (E5.5_Ref_2VE)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
2VE
E5.5_Ref_2VE

value: section 2 region VE


title: Stage E5.5 embryo 2 section 2 region A (E5.5_Ref_2A)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
2A
E5.5_Ref_2A


title: Stage E5.5 embryo 2 section 2 region P (E5.5_Ref_2P)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
2P
E5.5_Ref_2P


title: Stage E6.0 embryo 2 section 2 region P (E6.0_Ref_2B)

description:
E6.0_Embryo2_Ref.all.samples.genes.fpkm.txt
2P
E6.0_Ref_2B


title: Stage E5.5 embryo 1 section 6 region P (E5.5_1_6B)

description:
E5.5_Embryo1_all.samples.genes.fpkm.txt
6P
E5.5_1_6B

value: section 6 region P


title: Stage E5.5 embryo 2 section 1 region VE (E5.5_Ref_1VE)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
1VE
E5.5_Ref_1VE

value: section 1 region VE


title: Stage E5.5 embryo 2 section 1 region AP (E5.5_Ref_1AP)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
1AP
E5.5_Ref_1AP


title: Stage E5.5 embryo 1 section 6 region A (E5.5_1_6A)

description:
E5.5_Embryo1_all.samples.genes.fpkm.txt
6A
E5.5_1_6A

value: section 6 region A


title: Stage E5.5 embryo 1 section 5 region A (E5.5_1_5A)

description:
E5.5_Embryo1_all.samples.genes.fpkm.txt
5A
E5.5_1_5A


title: Stage E5.5 embryo 1 section 4 region P (E5.5_1_4B)

description:
E5.5_Embryo1_all.samples.genes.fpkm.txt
4P
E5.5_1_4B

value: section 4 region P


title: Stage E5.5 embryo 1 section 4 region A (E5.5_1_4A)

description:
E5.5_Embryo1_all.samples.genes.fpkm.txt
4A
E5.5_1_4A

value: section 4 region A


title: Stage E5.5 embryo 1 section 5 region P (E5.5_1_5B)

description:
E5.5_Embryo1_all.samples.genes.fpkm.txt
5P
E5.5_1_5B


title: Stage E5.5 embryo 1 section 3 region A (E5.5_1_3A)

description:
E5.5_Embryo1_all.samples.genes.fpkm.txt
3A
E5.5_1_3A


title: Stage E5.5 embryo 2 section 6 region P (E5.5_Ref_6P)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
6P
E5.5_Ref_6P


title: Stage E5.5 embryo 1 section 3 region P (E5.5_1_3B)

description:
E5.5_Embryo1_all.samples.genes.fpkm.txt
3P
E5.5_1_3B

value: section 3 region P


title: Stage E5.5 embryo 1 section 2 region P (E5.5_1_2B)

description:
E5.5_Embryo1_all.samples.genes.fpkm.txt
2P
E5.5_1_2B


title: Stage E5.5 embryo 2 section 6 region A (E5.5_Ref_6A)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
6A
E5.5_Ref_6A


title: Stage E5.5 embryo 2 section 4 region A (E5.5_Ref_4A)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
4A
E5.5_Ref_4A


title: Stage E5.5 embryo 1 section 1 region AP (E5.5_1_1)

description:
E5.5_Embryo1_all.samples.genes.fpkm.txt
1AP
E5.5_1_1


title: 2D2 NIKΔT

city: Mainz

first: Tobias

last: Bopp

address: Langenbeckstrasse 1

department: Institute for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequence and further processed using the software CLC genomics workbench (6.5; using CLC's default settings for RNA-Seq analysis). Reads were aligned to mm9 genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated employing CLC Genomics Workbench (6.5)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Vβ11+CD4+CD90.1+CD90.2+ (2D2 NIK∆T) cells

growth_protocol: generation of mBMCs  protocol: Recipient C57BL/6 Ly5.1 mice were lethally irradiated with 9.5 Gray and reconstituted by i.v. injection of 5x10^6 2D2NIKflfl (CD90.1) and 5x10^6 2D2NIKΔT (CD90.1/2) BM cells. The BM of mixed BMCs could be distinguished according to the congenic marker CD90.1 and CD90.1/2.

extract_protocol:
T cell total RNA was isolated using Rneasy midi kit (Qiagen)
RNA libraries were prepared for sequencing using standard NEBnext Ultra RNA lib prep kit for Illumina protocol using 12 PCR cycles for final amplification.

treatment_protocol: After BM reconstitution mice were immunized subcutaneously at the base of the tail with 50μg MOG35‐55 peptide (Gene Script, amino acid sequence: MEVGWYRSPFSRVVHLYRNGK) emulsified in complete Freund’s adjuvant (Difco) supplemented with 1.1 mg of heat‐inactivated Mycobacterium tuberculosis (Difco). 4 days later live Vβ11+CD4+CD90.1+ (NIKflfl) or live Vβ11+CD4+CD90.1+CD90.2+ (NIK∆T) cells were sorted.

tag: strain background

tag: genotype/variation

value: deficiency of MAP3K14; 2D2+/-; CD90.1/2

value: in vivo (4days MOG/CFA) activated 2D2 NIK{delta}T T cells


title: Stage E5.5 embryo 2 section 3 region A (E5.5_Ref_3A)

description:
E5.5_Embryo2.ref.gene.fpkm.txt
3A
E5.5_Ref_3A

value: section 3 region A


title: Lu-TC3

city: chengdu

first: Mingzhou

last: Li

state: Sichuan

address: No.211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
Illumina Casava1.82 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to itself assembly genome using Tophat.
Cufflinks version 2.2.1 were applied to quantify gene expression and obtain FPKM expression values (denoted as the fragments per Kb of transcript per Mb mapped reads).
Genome_build: Gallus_gallus.Galgal4.78
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Gallus gallus

source_name: Lung

extract_protocol:
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: altitude

tag: tissue

value: Lung


title: Lu-LTC1


title: Lu-LTC2


title: Lu-TC2


title: Lu-TC1


title: Lu-LC3


title: Lu-HLC2


title: Lu-HLC1


title: Lu-LC1


title: Li-TC2

source_name: Liver

value: Liver


title: Li-LTC3


title: Stage E5.5 embryo 1 section 2 region A (E5.5_1_2A)

description:
E5.5_Embryo1_all.samples.genes.fpkm.txt
2A
E5.5_1_2A

value: Pre-gastrulation embryo (E5.5)

value: section 2 region A


title: Li-LC3


title: Li-LC2


title: Li-LTC1


title: Li-HLC3


title: 2D2 NIKflfl

source_name: Vβ11+CD4+CD90.1+ (2D2 NIKflfl) cells

value: no deficiency of MAP3K14; 2D2+/-; CD90.1/1

value: in vivo (4days MOG/CFA) activated 2D2 NIKflfl T cells


title: Lu-LTC3


title: Li-HLC1


title: Li-LC1


title: H-TC2

source_name: Heart

value: Heart


title: Li-LTC2


title: H-TC3


title: Li-HLC2


title: Li-TC3


title: H-LTC3


title: H-TC1


title: H-LTC2


title: Lu-LC2


title: H-LC2


title: H-LC1


title: H-LC3


title: H-HLC3


title: H-LTC1


title: Li-TC1


title: H-HLC2


title: B-TC1

source_name: Brain

value: Brain


title: B-TC2


title: B-LTC3


title: B-TC3


title: B-LTC1


title: H-HLC1


title: B-LTC2


title: B-LC3


title: B-LC2


title: B-LC1


title: B-HLC3


title: B-HLC2


title: B-HLC1


title: C57BL6/Pdk2KO_PBS_10

city: San Diego

first: Sole

last: Gatto

state: CA

address: 12636 High Bluff Drive, Suite 400

country: USA

institute: Monoceros Biosystems

data_processing:
Data was collected using the NextSeq 500 sequencer per manufacturer's protocol (Illumina).
Sequencing quality was assessed with the FastQC tool v0.11.2 and trimmed with TrimGalore. Reads were mapped using STAR with samtools v1.1.
HTSeq v0.6.1 was used to generate counts. Map and count quality was assessed by picard tools v1.119 and RSeQC tool.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Raw counts per gene

molecule: polyA RNA

source_name: kidney

extract_protocol:
Kidneys were removed, flash frozen on dry ice, and RNA was harvested using Qiagen RNeasy kit
TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Pkd2-KO mice were dosed SC with PBS or 20 mg kg-1 of RGLS4326 at post-natal day (P)10, P11, P12, and P19; and kidneys were harvested on P28

value: kidney

tag: treatment

value: PBS

tag: dose

tag: background strain

tag: genotype


title: C57BL6/Pdk2KO_PBS_9


title: C57BL6/Pdk2KO_RGLS4326_11


title: C57BL6_6

value: No treatment

value: wildtype


title: C57BL6/Pdk2KO_RGLS4326_9


title: C57BL6/Pdk2KO_PBS_8


title: C57BL6/Pdk2KO_RGLS4326_10


title: C57BL6_12


title: C57BL6_5


title: C57BL6_10


title: C57BL6_9


title: C57BL6_7


title: C57BL6_8


title: C57BL6/Pdk2KO_PBS_7


title: C57BL6/Pdk2KO_RGLS4326_8


title: C57BL6/Pdk2KO_PBS_5


title: C57BL6/Pdk2KO_PBS_6


title: C57BL6/Pdk2KO_PBS_4


title: C57BL6/Pdk2KO_RGLS4326_6


title: C57BL6_4


title: C57BL6_11


title: C57BL6/Pdk2KO_RGLS4326_7


title: C57BL6_2


title: C57BL6_1


title: C57BL6/Pdk2KO_PBS_3


title: C57BL6/Pdk2KO_PBS_11


title: C57BL6/Pdk2KO_PBS_2


title: Lu-HLC3


title: CD1_2

extract_protocol:
Kidneys were removed, flash frozen on dry ice, and RNA was harvested using  Qiagen RNeasy kit
TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Five-weeks-old Pcy/CD1 mice were treated with subcutaneous injections of either PBS or RGLS4326 at 25 mg kg-1 monthly  for 25-weeks. Five age-matched untreated male WT/CD1 mice were included for comparison


title: C57BL6/Pdk2KO_RGLS4326_1


title: CD1_3


title: C57BL6/Pdk2KO_PBS_1


title: CD1_5


title: C57BL6/Pdk2KO_RGLS4326_3


title: C57BL6/Pdk2KO_RGLS4326_2


title: CD1_4


title: CD1_1


title: Pcy_RGLS4326_5-30_M_11

value: monthly, from 5 to 30 weeks


title: Pcy_RGLS4326_5-30_M_9


title: Pcy_RGLS4326_5-30_M_13


title: C57BL6_3


title: Pcy_RGLS4326_5-30_M_7


title: C57BL6/Pdk2KO_RGLS4326_5


title: Pcy_RGLS4326_5-30_M_5


title: Pcy_PBS_12

value: weekly


title: Pcy_RGLS4326_5-30_M_4


title: Pcy_RGLS4326_5-30_M_8


title: Pcy_RGLS4326_5-30_M_1


title: Pcy_PBS_11


title: Pcy_RGLS4326_5-30_M_3


title: C57BL6/Pdk2KO_RGLS4326_4


title: Pcy_PBS_9


title: Pcy_PBS_10


title: Pcy_PBS_5


title: Pcy_PBS_3


title: Pcy_PBS_7


title: Pcy_PBS_2


title: Pcy_RGLS4326_5-30_M_14


title: Pcy_PBS_8


title: Pcy_RGLS4326_5-30_M_2


title: Lin-CD45-Cd71- Flushed, digested

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

country: Spain

institute: CRG

description: Flushed.BM.Digested

data_processing:
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
CellRanger 2.0.0, 10x genomics, Pleasanton, CA
Filtering of cells with less than 500 genes observed or more than 5% of molecules stemming from mitochondrial RNA. R-3.5.0, Seurat-2.3.3
Genome_build: mm10, cellranger version 1.2.0
Supplementary_files_format_and_content: Comma-separated value files of molecule (UMI) counts containing cells (post-filtering) in columns and genes in rows

source_name: Flushed bone marrow

extract_protocol:
Fresh bone marrow cells were isolated by flushing of long bones. Marrow was then enzymatically digested using collagenase I and dispase. Cells were stained with fluorescently labelled antibodies against lineage markers (CD4, CD8, CD11b, B220, Gr1, Ter119), CD71 and CD45. A DNA dye was used to exclude debris. Single Lin-CD45-CD71-DNA+ cells were sorted into PBS-2%FCS. Full-length cDNA from individual cells were produced following the Chromium Single Cell 3’ Reagent v2 protocol (10x genomics, Pleasanton, CA) according to manufacturer’s recommendations.
Default library production protocol, 10x genomics, Pleasanton, CA

tag: bm isolation

value: Bone flushing

tag: digestion

value: Yes


title: Pcy_PBS_6


title: Pcy_RGLS4326_5-30_M_6


title: Pcy_PBS_4


title: Bone marrow cells, P2CD61minusH5

data_processing:
Adapter trimming, perl
Pseudoalignment, kallisto 0.43.0
Count tables, R 3.5.1/scater 1.10.1
Genome_build: Mus Musculus mm10, ENSEMBL release 38.91
Supplementary_files_format_and_content: counts.csv, .tsv (Kallisto output)

source_name: Bone Marrow

extract_protocol:
Fresh bone marrow cells were isolated by crushing mouse bones in media supplemented with FCS and the supernatant was collected. Cells were stained with fluorescently labelled antibodies (CD45, Ter119, CD41, CD71, CD51, CD61, CD200, VCAM1) . A vibrant dye was used to exclude debris. Single cells were sorted into 96-well-plates in Smart-seq2 lysis buffer. Full-length cDNA from individual cells were produced following the SmartSeq2 protocol.
Tagmentation using Homemade Tn5 (Hennig et al., G3 2018)

value: Bone Marrow

tag: sorting gate


title: Pcy_RGLS4326_5-30_M_10


title: Bone marrow cells, P2CD61minusF8


title: Bone marrow cells, P310XA11


title: Bone marrow cells, P2CD61minusG6


title: Bone marrow cells, P2CD61minusF5


title: Bone marrow cells, P2CD61minusE9


title: Bone marrow cells, P2CD61minusE4


title: Lin-CD45-Cd71- Flushed, non-digested

description: Flushed.BM.NonDigested

extract_protocol:
Fresh bone marrow cells were isolated by flushing of long bones. Cells were stained with fluorescently labelled antibodies against lineage markers (CD4, CD8, CD11b, B220, Gr1, Ter119), CD71 and CD45. A DNA dye was used to exclude debris. Single Lin-CD45-CD71-DNA+ cells were sorted into PBS-2%FCS. Full-length cDNA from individual cells were produced following the Chromium Single Cell 3’ Reagent v2 protocol (10x genomics, Pleasanton, CA) according to manufacturer’s recommendations.
Default library production protocol, 10x genomics, Pleasanton, CA

value: No


title: Bone marrow cells, P2CD61minusD5


title: Bone marrow cells, P2CD61minusD9


title: Bone marrow cells, P2CD61minusD4


title: Pcy_PBS_1


title: Bone marrow cells, P2CD61minusD10


title: Bone marrow cells, P2CD61minusC11


title: Bone marrow cells, P2CD61minusB6


title: Bone marrow cells, P2CD61minusD3


title: Bone marrow cells, P2CD61minusB11


title: Bone marrow cells, P2CD61minusF9


title: Bone marrow cells, P2CD61minusB2


title: Bone marrow cells, P2CD61minusA6


title: Bone marrow cells, P210XG1


title: Bone marrow cells, P210XC4


title: Bone marrow cells, P210XH8


title: Bone marrow cells, P210XG11


title: Bone marrow cells, P210XB7


title: Bone marrow cells, P210XG12


title: Bone marrow cells, P1CD61plusG9


title: Bone marrow cells, P1CD61plusE6


title: Bone marrow cells, P1CD61plusG5


title: Bone marrow cells, P1CD61plusG4


title: Bone marrow cells, P1CD61plusE11


title: Bone marrow cells, P1CD61plusC6


title: Bone marrow cells, P1CD61plusE10


title: Bone marrow cells, P1CD61plusC5


title: Bone marrow cells, P1CD61plusC3


title: Bone marrow cells, P1CD61plusC2


title: Bone marrow cells, P210XB4


title: Bone marrow cells, P1CD61plusB9


title: Bone marrow cells, P2CD61minusA8


title: Bone marrow cells, P1CD61plusB10


title: Bone marrow cells, P1CD61plusB1


title: Bone marrow cells, P210XB5


title: Bone marrow cells, P2CD61plusG4


title: Bone marrow cells, P1CD61plusA9


title: Bone marrow cells, P2CD61plusG3


title: Bone marrow cells, P1CD61plusF7


title: Bone marrow cells, P2CD61plusF8


title: Bone marrow cells, P2CD61plusF7


title: Bone marrow cells, P2CD61plusF4


title: Bone marrow cells, P2CD61plusF1


title: Bone marrow cells, P2CD61plusE8


title: Bone marrow cells, P2CD61minusA7


title: Bone marrow cells, P2CD61plusD3


title: Bone marrow cells, P2CD61plusE7


title: Bone marrow cells, P2CD61plusE6


title: Bone marrow cells, P2CD61plusD6


title: Bone marrow cells, P2CD61plusD7


title: Bone marrow cells, P2CD61plusC4


title: Bone marrow cells, P2CD61plusC5


title: Bone marrow cells, P2CD61plusB3


title: Bone marrow cells, P2CD61plusC9


title: Bone marrow cells, P2CD61plusG10


title: Bone marrow cells, P2CD61plusA6


title: Bone marrow cells, P2CD61plusA3


title: 9-WT

type: RNA

city: Denton

first: Lina

last: Gallego-Giraldo

state: Texas

address: 1155 Union Circle #311428

department: Biology

institute: University of north Texas, Biodiscovery Institute

description: total RNA from wild-type modified 1.5 months old plants

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Arabidopsis Genome Array (Affymetrix, http://www.affymetrix.com/) . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
Data normalization was conducted using robust multichip average (RMA) (Irizarry et al., 2003). The presence/absence call for each probe set was obtained from dCHIP (Li and Wong, 2001).  Genes with significantly different expression levels between the wild-type control and mutants were selected using associative analysis, as described by Dozmorov and Centola (Dozmorov and Centola, 2003). The type-I family-wise error rate was reduced by using a Bonferroni corrected P-value threshold of 0.05/N, where N represents the number of genes present on the chip. The false discovery rate was monitored and controlled by Q value (false discovery rate), calculated using Extraction of Differential Gene Expression (EDGE, http://www.biostat.washington.edu/software/
value normalized using robust multichip average (RMA) from MAS5.0 signal intensity

label: biotin

organism: Arabidopsis thaliana

source_name: Inflorescence stem

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seeds were exposed to 4˚C for 2 days and then sown in a seedling mix substrate (Metro-Mix 360, SUN GRO) with controlled fertilizer (20-10-20; 20%N, 10%P2O5 and 20%K2O at the dose 200 ppm per gallon at 21˚C under a 16h-light/8h-dark photoperiod. Light intensity was 110 µmol m-2 s-1, supplied by both incandescent and fluorescent lights.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.RNA was cleaned using the RNA cleanup kit (Qiagen)

treatment_protocol: Stems were harvested, frozen at -80C and ground

tag: ecotype

value: WT

value: Inflorescence stem


title: WA_6Mar19

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

data_processing:
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA). Reads were trimmed using cutadapt
Quality scores were assessed using FastQC
Reads were aligned to the Homo sapiens genome build hg19 using STAR
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression (RLE) using DESeq2 R library
Read Distribution percentages, heatmaps, and sample plots were generated as part of the QC step using RSeQC. DEseq2 was also used to calculate fold changes and p-values.
Genome_build: hg19
Supplementary_files_format_and_content: text files with Relative Log Expression (RLE) values for each sample

organism: Homo sapiens

source_name: Breast cancer cells

growth_protocol: MDA-MB231 cells were cultured in DMEM, 10% Fetal Bovine Serum (FBS), and 1% antibiotic/antimycotic

extract_protocol:
RNA from weakly and strongly adherent cells was purified using Qiagen RNeasy Mini Kit (Qiagen, 74104).
RNA quality was assessed using TapeStation (Agilent), RNA libraries were prepared using the Illumina TruSeq Stranded RNA, High Throughput Library Prep Kit and sequenced using the Illumina HiSeq 4000 system to generate 50 bp single-end reads.

tag: cell line

tag: adhesion strength

value: Weak


title: WA_15Mar19


title: WA_12Mar19


title: SA_15Mar19

value: Strong


title: HNLN1

city: Turku

first: Akira

last: Takeda

state: South-West Finland

address: Tykistökatu 6A

department: Institute of Biomedicine

country: Finland

institute: University of Turku

data_processing:
Post-processing including demultiplexing, read alignment and quality control was performed using the 10X Genomics Cell Ranger package (v2.0.0 or v2.1.1).
Genome_build: hg19
Supplementary_files_format_and_content: Cell Ranger-output files including one mtx file and two tsv files for gene ID and cell barcode ID.

source_name: HNLN1 lymphatic endothelial cells

extract_protocol:
Immediately after surgery, human LNs were transferred into RPMI on ice and cut into small pieces, and digested for 1h with RPMI containing collagenase P, dispase and DNase. Hematopoietic cells were depleted with EasySepTM Human CD45 Depletion Kit (Stem Cell Technologies), and the single cell suspension was incubated with PE-anti-PDPN, AF488-anti-CD45, APC-anti-CD31 and LIVE/DEADTM Fixable Near-IR Dead Cell Stain kit (ThermoFisher Scientific, L10119) for 30 min. Live CD45- PDPN+ CD31+ cells known to include LECs were sorted with FACS Aria (BD Bioscience) or SH800S (Sony) into RPMI medium containing 10% FCS. Sorted cells were immediately count and run on the 10X Chromium (10X Genomics).
ScRNAseq libraries were prepared according to the manufacturer’s instructions (CG00052 RevB) using Chromium™ Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics, 120237) and Chromium™ Single Cell A Chip Kit (10X Genomics, 120236).

value: Head and neck lymph node

tag: individual

value: Individual 4

value: LN CD45- PDPN+ CD31+ cells


title: HNLN2

source_name: HNLN2 lymphatic endothelial cells

value: Individual 5

tag: cell type


title: Bone marrow cells, P2CD61plusB4

tag: strain


title: Bone marrow cells, P2CD61plusA12


title: Bone marrow cells, P1CD61minusH9


title: Bone marrow cells, P2CD61plusA2


title: AXLN3

source_name: AXLN3 lymphatic endothelial cells

value: Axillary lymph node

value: Individual 2


title: SA_6Mar19


title: Bone marrow cells, P1CD61minusH6


title: AXLN4

source_name: AXLN4 lymphatic endothelial cells

value: Individual 3


title: 7-WT


title: 5-CCR

description: total RNA from lignin modified 1.5 months old plants

value: loss of function ccr-1 mutant


title: AXLN2

source_name: AXLN2 lymphatic endothelial cells

value: Individual 1


title: 6-CCR


title: 3-HCT

value: HCT-RNAi


title: AXLN1

source_name: AXLN1 lymphatic endothelial cells


title: ESI-017 CoMo-NPC 3

first: Samuel

middle: L

last: Pfaff

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Human ES-derived NPC samples were aligned to hg19 using STAR with default settings. Rat samples with human grafts were aligned to both human (hg19) and rat (rn5) genomes. Aligned reads were assigned as either rat or human sourced based on their alignment scores to the two genomes. Reads that aligned equally well were discarded as ambiguous.
Human aligned reads and rat aligned reads were converted to wig format via Bedtools. The ‘coverage’ function was called using ‘-split -abam’ flags. Wigs were convered to bigWig format with UCSC tools
Genome_build: hg19 and rn5
Supplementary_files_format_and_content: All processed files are bigWig format. Rat samples have two processed files each: one for the estimated human sourced reads and a second for the estimated rat source reads

source_name: Human

extract_protocol:
RNA was isolated from in vitro cultured NPCs or NPC-grafted spinal cord specimens using the miRvana miRNA isolation kit (Ambion AM1560). The protocol for total RNA collection was used.
Paired-end 100 bp or single-end 75 bp RNA sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions

value: ES derived NPC

tag: graft age

value: ESI-017 ES-derived neural progenitor cell

tag: batch


title: 1-HCT


title: 2-HCT


title: Bone marrow cells, P1CD61minusH5

value: Bone Marrow


title: Bone marrow cells, P1CD61minusG9


title: 8-WT

value: WT


title: ESI-017 CoMo-NPC 2


title: ESI-017 CoMo-NPC 4


title: ESI-017 CoMo-NPC 1


title: Stage E7.0 endoderm single cell plate 4H7 cell (E7.0SCVE4-H7)

description: processed data file: E7.0SingleCell.tpm.txt

source_name: Mouse embryonic cells

tag: developmental stage

value: Mid-gastrulation embryo (E7.0)

tag: tag

value: Mouse embryonic cells


title: Bone marrow cells, P1CD61plusD2

tag: tissue


title: Stage E7.0 endoderm single cell plate 4H9 cell (E7.0SCVE4-H9)


title: Bone marrow cells, P1CD61minusG6


title: Stage E7.0 endoderm single cell plate 4H6 cell (E7.0SCVE4-H6)


title: Bone marrow cells, P1CD61minusG7


title: Stage E7.0 endoderm single cell plate 4H8 cell (E7.0SCVE4-H8)


title: Bone marrow cells, P1CD61minusG4


title: Stage E7.0 endoderm single cell plate 4H5 cell (E7.0SCVE4-H5)


title: Bone marrow cells, P1CD61minusG2


title: Stage E7.0 endoderm single cell plate 4H3 cell (E7.0SCVE4-H3)


title: Stage E7.0 endoderm single cell plate 4H1 cell (E7.0SCVE4-H1)


title: pt2385_21_perc_rep3

city: Lund

first: Kristoffer

last: von Stedingk

address: Scheelevägen 2

country: Sweden

institute: Lund University

data_processing:
Library preparation using TruSeq stranded mRNA sample preparation kit
Sequencing of libraries was performed using HiSeq2500 high output mode and v4 chemistry
Raw sequences (fastq files) were aligned using HiSat2 to the hg19 human genome build
Expression matrix of HiSat2 output was produced using cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: gene based expression matrix of cufflinks processed count data (value of 1 was added to all measurements)

source_name: Neuroblastoma Patient Derived Orthotopic Xenograft cells

growth_protocol: PDX-derived cells were continuously kept in a mix of Dulbecco’s Modified Eagle’s Medium (DMEM) and GlutaMAXTM F-12 (3:1 ratio) supplemented with 1% penicillin/streptomycin (P/S), 2% B27 w/o vitamin A, 40 ng/ul basic Fibroblast Growth Factor (FGF) and 20 ng/ul Epidermal Growth Factor (EGF), with no addition of FBS.

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq stranded mRNA sample preparation kit

treatment_protocol: Neuroblastoma PDX cells were treated with 1mM PT2385 directly after seeding in hypoxic (21% oxygen) or normoxic (0.1% oxygen) conditions, and once more at 24 hours post seeding.

tag: agent

tag: group

value: normoxia


title: pt2385_01_perc_rep3

value: hypoxia


title: dmso_21_perc_rep3

value: DMSO


title: Stage E7.0 endoderm single cell plate 4H12 cell (E7.0SCVE4-H12)


title: Bone marrow cells, P1CD61minusG11


title: pt2385_01_perc_rep2


title: Pcy_RGLS4326_5-30_M_12

value: kidney

tag: treatment

tag: dose

value: monthly, from 5 to 30 weeks


title: Stage E7.0 endoderm single cell plate 4H10 cell (E7.0SCVE4-H10)


title: Bone marrow cells, P1CD61minusF8


title: Stage E7.0 endoderm single cell plate 4G9 cell (E7.0SCVE4-G9)


title: dmso_01_perc_rep2


title: Stage E7.0 endoderm single cell plate 4H4 cell (E7.0SCVE4-H4)


title: Stage E7.0 endoderm single cell plate 4G8 cell (E7.0SCVE4-G8)


title: Stage E7.0 endoderm single cell plate 4H2 cell (E7.0SCVE4-H2)


title: pt2385_21_perc_rep2


title: Stage E7.0 endoderm single cell plate 4G6 cell (E7.0SCVE4-G6)


title: Stage E7.0 endoderm single cell plate 4G7 cell (E7.0SCVE4-G7)


title: Stage E7.0 endoderm single cell plate 4G5 cell (E7.0SCVE4-G5)


title: Bone marrow cells, P1CD61minusF3


title: Bone marrow cells, P1CD61minusF7


title: dmso_21_perc_rep2


title: Stage E7.0 endoderm single cell plate 4G2 cell (E7.0SCVE4-G2)


title: Stage E7.0 endoderm single cell plate 4G4 cell (E7.0SCVE4-G4)


title: Stage E7.0 endoderm single cell plate 4G3 cell (E7.0SCVE4-G3)


title: Bone marrow cells, P1CD61minusF2


title: dmso_21_perc_rep1


title: Stage E7.0 endoderm single cell plate 4G12 cell (E7.0SCVE4-G12)


title: dmso_01_perc_rep3


title: Stage E7.0 endoderm single cell plate 4H11 cell (E7.0SCVE4-H11)


title: Bone marrow cells, P1CD61minusE3


title: Bone marrow cells, P1CD61minusF10


title: Stage E7.0 endoderm single cell plate 4G1 cell (E7.0SCVE4-G1)


title: pt2385_01_perc_rep1


title: Stage E7.0 endoderm single cell plate 4G11 cell (E7.0SCVE4-G11)


title: dmso_01_perc_rep1


title: Stage E7.0 endoderm single cell plate 4F9 cell (E7.0SCVE4-F9)


title: Stage E7.0 endoderm single cell plate 4G10 cell (E7.0SCVE4-G10)


title: Bone marrow cells, P1CD61plusB5


title: Bone marrow cells, P1CD61minusD8


title: Bone marrow cells, P1CD61minusD7


title: Stage E7.0 endoderm single cell plate 4F7 cell (E7.0SCVE4-F7)


title: Stage E7.0 endoderm single cell plate 4F8 cell (E7.0SCVE4-F8)


title: pt2385_21_perc_rep1


title: Bone marrow cells, P1CD61minusD5


title: Bone marrow cells, P1CD61minusD3


title: Stage E7.0 endoderm single cell plate 4F2 cell (E7.0SCVE4-F2)


title: Stage E7.0 endoderm single cell plate 4F4 cell (E7.0SCVE4-F4)


title: Stage E7.0 endoderm single cell plate 4F5 cell (E7.0SCVE4-F5)


title: Stage E7.0 endoderm single cell plate 4F3 cell (E7.0SCVE4-F3)


title: Stage E7.0 endoderm single cell plate 4F6 cell (E7.0SCVE4-F6)


title: 4-CCR

tag: genotype

value: Inflorescence stem


title: Stage E7.0 endoderm single cell plate 4F11 cell (E7.0SCVE4-F11)


title: Stage E7.0 endoderm single cell plate 4F10 cell (E7.0SCVE4-F10)


title: Stage E7.0 endoderm single cell plate 4E9 cell (E7.0SCVE4-E9)


title: Stage E7.0 endoderm single cell plate 4E8 cell (E7.0SCVE4-E8)


title: Bone marrow cells, P1CD61minusC7

tag: sorting gate


title: Bone marrow cells, P1CD61minusC9


title: Stage E7.0 endoderm single cell plate 4F1 cell (E7.0SCVE4-F1)


title: Stage E7.0 endoderm single cell plate 4F12 cell (E7.0SCVE4-F12)


title: Stage E7.0 endoderm single cell plate 4E7 cell (E7.0SCVE4-E7)


title: Stage E7.0 endoderm single cell plate 4E6 cell (E7.0SCVE4-E6)


title: Bone marrow cells, P1CD61minusC3


title: Bone marrow cells, P1CD61minusC6


title: Stage E7.0 endoderm single cell plate 4E5 cell (E7.0SCVE4-E5)


title: Clone c, 4OHT treated for 4hrs [mRNA_TC]

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

description:
rRNA depleted RNA
4h_c

data_processing:
Reads were mapped using STAR, removing multi-mappers
Count tables were generated using featureCounts
fold change vaues were determined using the Deseq package
Genome_build: mm10

source_name: mouse embryonic stem cells expressing a cRAF-ERT2 construct allowing ERK activation upon the addition of 4OT

growth_protocol: mESCs were grown in serum containing medium, supplemented with 1x LIF (made in house) and 2uM Chir99021. 24hrs prior to treatment, media was changed to serum containing media supplemented with 1x LIF and 250nM PD173074.

extract_protocol:
Total RNA was collected using  the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by DNAse treatment (Qiagen). rRNA was removed using the RiboGold kit (Illumina)
Libraries were prepared using the NEB Next Ultra 2 kit.

treatment_protocol: Cells were left untreated (0h), or treated with 250nM 4OHT (2h). 15 minutes prior to RNA isolation cells were treated with 5mM ethynyl uridine to label newly synthesized RNA.

value: 4OHT treated for 4hrs

tag: background strain

tag: Stage

value: embryonic


title: Stage E7.0 endoderm single cell plate 4E4 cell (E7.0SCVE4-E4)


title: Stage E7.0 endoderm single cell plate 4E12 cell (E7.0SCVE4-E12)


title: Stage E7.0 endoderm single cell plate 4E3 cell (E7.0SCVE4-E3)


title: Clone b, 4OHT treated for 4hrs [mRNA_TC]

description:
rRNA depleted RNA
4h_b

value: mouse embryonic stem cells expressing a cRAF-ERT2 construct allowing ERK activation upon the addition of 4OT


title: Stage E7.0 endoderm single cell plate 4E1 cell (E7.0SCVE4-E1)


title: Stage E7.0 endoderm single cell plate 4E2 cell (E7.0SCVE4-E2)


title: Clone a, 4OHT treated for 4hrs [mRNA_TC]

description:
rRNA depleted RNA
4h_a


title: Bone marrow cells, P1CD61minusD2


title: Clone c, 4OHT treated for 2hrs [mRNA_TC]

description:
rRNA depleted RNA
2h_c

value: 4OHT treated for 2hrs


title: Stage E7.0 endoderm single cell plate 4D9 cell (E7.0SCVE4-D9)


title: Clone b, 4OHT treated for 2hrs [mRNA_TC]

description:
rRNA depleted RNA
2h_b


title: Stage E7.0 endoderm single cell plate 4D8 cell (E7.0SCVE4-D8)


title: Stage E7.0 endoderm single cell plate 4D6 cell (E7.0SCVE4-D6)


title: Clone a, 4OHT treated for 2hrs [mRNA_TC]

description:
rRNA depleted RNA
2h_a


title: Clone b, 4OHT treated for 1hr [mRNA_TC]

description:
rRNA depleted RNA
1h_b

value: 4OHT treated for 1hr


title: Clone c, 4OHT treated for 1hr [mRNA_TC]

description:
rRNA depleted RNA
1h_c


title: Stage E7.0 endoderm single cell plate 4D2 cell (E7.0SCVE4-D2)


title: Stage E7.0 endoderm single cell plate 4D1 cell (E7.0SCVE4-D1)


title: Stage E7.0 endoderm single cell plate 4D4 cell (E7.0SCVE4-D4)


title: Stage E7.0 endoderm single cell plate 4D12 cell (E7.0SCVE4-D12)


title: Clone a, 4OHT treated for 1hr [mRNA_TC]

description:
rRNA depleted RNA
1h_a


title: Clone c, untreated [mRNA_TC]

description:
rRNA depleted RNA
0h_c

value: untreated


title: Stage E7.0 endoderm single cell plate 4D11 cell (E7.0SCVE4-D11)


title: Stage E7.0 endoderm single cell plate 4D10 cell (E7.0SCVE4-D10)


title: Stage E7.0 endoderm single cell plate 4C9 cell (E7.0SCVE4-C9)


title: Clone b, untreated [mRNA_TC]

description:
rRNA depleted RNA
0h_b


title: Stage E7.0 endoderm single cell plate 4C8 cell (E7.0SCVE4-C8)


title: Stage E7.0 endoderm single cell plate 4C6 cell (E7.0SCVE4-C6)


title: Clone a, untreated [mRNA_TC]

description:
rRNA depleted RNA
0h_a


title: Stage E7.0 endoderm single cell plate 4E11 cell (E7.0SCVE4-E11)


title: Stage E7.0 endoderm single cell plate 4C7 cell (E7.0SCVE4-C7)


title: Stage E7.0 endoderm single cell plate 4D7 cell (E7.0SCVE4-D7)


title: Stage E7.0 endoderm single cell plate 4C5 cell (E7.0SCVE4-C5)


title: Stage E7.0 endoderm single cell plate 4C4 cell (E7.0SCVE4-C4)


title: Stage E7.0 endoderm single cell plate 4C11 cell (E7.0SCVE4-C11)


title: Stage E7.0 endoderm single cell plate 4C2 cell (E7.0SCVE4-C2)


title: Stage E7.0 endoderm single cell plate 4C3 cell (E7.0SCVE4-C3)


title: Stage E7.0 endoderm single cell plate 4D5 cell (E7.0SCVE4-D5)


title: Stage E7.0 endoderm single cell plate 4E10 cell (E7.0SCVE4-E10)


title: Stage E7.0 endoderm single cell plate 4C12 cell (E7.0SCVE4-C12)


title: Stage E7.0 endoderm single cell plate 4C1 cell (E7.0SCVE4-C1)


title: Stage E7.0 endoderm single cell plate 4D3 cell (E7.0SCVE4-D3)


title: Stage E7.0 endoderm single cell plate 4B9 cell (E7.0SCVE4-B9)


title: Stage E7.0 endoderm single cell plate 4B7 cell (E7.0SCVE4-B7)


title: Stage E7.0 endoderm single cell plate 4B8 cell (E7.0SCVE4-B8)


title: Stage E7.0 endoderm single cell plate 4C10 cell (E7.0SCVE4-C10)


title: Stage E7.0 endoderm single cell plate 4B6 cell (E7.0SCVE4-B6)


title: Stage E7.0 endoderm single cell plate 4B5 cell (E7.0SCVE4-B5)


title: Stage E7.0 endoderm single cell plate 4B4 cell (E7.0SCVE4-B4)


title: Stage E7.0 endoderm single cell plate 4B3 cell (E7.0SCVE4-B3)


title: Stage E7.0 endoderm single cell plate 4B1 cell (E7.0SCVE4-B1)


title: Stage E7.0 endoderm single cell plate 4B2 cell (E7.0SCVE4-B2)


title: Stage E7.0 endoderm single cell plate 4B12 cell (E7.0SCVE4-B12)


title: Stage E7.0 endoderm single cell plate 4B11 cell (E7.0SCVE4-B11)


title: Stage E7.0 endoderm single cell plate 4B10 cell (E7.0SCVE4-B10)


title: 8h_WT_clone B +DOX

description:
nascent RNA
8h_WT_B

data_processing:
Reads were mapped using STAR, removing multi-mappers
Count tables were generated using featureCounts
fold change vaues (0h/2h) (0h/8h) were determined using the Deseq package
Genome_build: mm10

source_name: mouse embryonic stem cells

extract_protocol:
Total RNA was collected using  the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by DNAse treatment (Qiagen). Nascent RNA was purified using the Click-iT Nascent RNA Capture Kit (Invitrogen)
Libraries were prepared using the NEB Next Ultra 2 kit.

treatment_protocol: Cells were left untreated (0h DMSO), or treated with 250nM 4OHT (2h, DMSO), or treated with either PD302509 or PP1, or in combination with 4OHT for 2hrs. 15 minutes prior to RNA isolation cells were treated with 5mM ethynyl uridine to label newly synthesized RNA.

value: mouse embryonic stem cells

value: 8h 4OHT

tag: genotype/variation

value: Med24 KO cells rescued with TET-Med24 cDNA


title: Stage E7.0 endoderm single cell plate 4A9 cell (E7.0SCVE4-A9)

value: Mid-gastrulation embryo (E7.0)


title: 8h_WT_clone C +DOX

description:
nascent RNA
8h_WT_C


title: 8h_WT_clone A +DOX

description:
nascent RNA
8h_WT_A


title: Stage E7.0 endoderm single cell plate 4A8 cell (E7.0SCVE4-A8)

value: Mouse embryonic cells


title: Stage E7.0 endoderm single cell plate 4A6 cell (E7.0SCVE4-A6)


title: Stage E7.0 endoderm single cell plate 4A7 cell (E7.0SCVE4-A7)


title: Stage E7.0 endoderm single cell plate 4A3 cell (E7.0SCVE4-A3)


title: Stage E7.0 endoderm single cell plate 4A5 cell (E7.0SCVE4-A5)


title: Stage E7.0 endoderm single cell plate 4A2 cell (E7.0SCVE4-A2)


title: Stage E7.0 endoderm single cell plate 4A1 cell (E7.0SCVE4-A1)


title: 8h_KO clone B -DOX

description:
nascent RNA
8h_KO_B

value: Med24 KO cells


title: Stage E7.0 endoderm single cell plate 4A12 cell (E7.0SCVE4-A12)


title: Stage E7.0 endoderm single cell plate 4A11 cell (E7.0SCVE4-A11)


title: 8h_KO clone A -DOX

description:
nascent RNA
8h_KO_A


title: 2h_WT_clone C +DOX

description:
nascent RNA
2h_WT_C

value: 2h 4OHT


title: 2h_WT_clone A +DOX

description:
nascent RNA
2h_WT_A


title: Stage E7.0 endoderm single cell plate 3H7 cell (E7.0SCVE3-H7)


title: Stage E7.0 endoderm single cell plate 3H9 cell (E7.0SCVE3-H9)


title: Stage E7.0 endoderm single cell plate 3H8 cell (E7.0SCVE3-H8)


title: 2h_KO clone C -DOX

description:
nascent RNA
2h_KO_C


title: Stage E7.0 endoderm single cell plate 3H4 cell (E7.0SCVE3-H4)


title: 2h_KO clone B -DOX

description:
nascent RNA
2h_KO_B


title: Stage E7.0 endoderm single cell plate 3H3 cell (E7.0SCVE3-H3)


title: 8h_KO clone C -DOX

description:
nascent RNA
8h_KO_C


title: Stage E7.0 endoderm single cell plate 3H2 cell (E7.0SCVE3-H2)


title: Stage E7.0 endoderm single cell plate 3H1 cell (E7.0SCVE3-H1)


title: 2h_KO clone A -DOX

description:
nascent RNA
2h_KO_A


title: 0h_WT_clone C +DOX

description:
nascent RNA
0h_WT_C

value: 0h 4OHT


title: Stage E7.0 endoderm single cell plate 3H12 cell (E7.0SCVE3-H12)


title: Stage E7.0 endoderm single cell plate 4A4 cell (E7.0SCVE4-A4)


title: Stage E7.0 endoderm single cell plate 3H11 cell (E7.0SCVE3-H11)


title: Stage E7.0 endoderm single cell plate 3G8 cell (E7.0SCVE3-G8)


title: Stage E7.0 endoderm single cell plate 3G9 cell (E7.0SCVE3-G9)


title: 0h_WT_clone B +DOX

description:
nascent RNA
0h_WT_B


title: Stage E7.0 endoderm single cell plate 3H10 cell (E7.0SCVE3-H10)


title: Stage E7.0 endoderm single cell plate 4A10 cell (E7.0SCVE4-A10)


title: 2h_WT_clone B +DOX

description:
nascent RNA
2h_WT_B


title: 0h_WT_clone A +DOX

description:
nascent RNA
0h_WT_A


title: Stage E7.0 endoderm single cell plate 3H6 cell (E7.0SCVE3-H6)


title: Stage E7.0 endoderm single cell plate 3G5 cell (E7.0SCVE3-G5)


title: 0h_KO clone B -DOX

description:
nascent RNA
0h_KO_B


title: Stage E7.0 endoderm single cell plate 3H5 cell (E7.0SCVE3-H5)


title: Stage E7.0 endoderm single cell plate 3G4 cell (E7.0SCVE3-G4)


title: Stage E7.0 endoderm single cell plate 3G3 cell (E7.0SCVE3-G3)


title: 0h_KO clone A -DOX

description:
nascent RNA
0h_KO_A


title: Stage E7.0 endoderm single cell plate 3G2 cell (E7.0SCVE3-G2)


title: Stage E7.0 endoderm single cell plate 3G1 cell (E7.0SCVE3-G1)


title: Stage E7.0 endoderm single cell plate 3G11 cell (E7.0SCVE3-G11)


title: Stage E7.0 endoderm single cell plate 3G10 cell (E7.0SCVE3-G10)


title: Stage E7.0 endoderm single cell plate 3F9 cell (E7.0SCVE3-F9)


title: Stage E7.0 endoderm single cell plate 3F7 cell (E7.0SCVE3-F7)


title: Stage E7.0 endoderm single cell plate 3F5 cell (E7.0SCVE3-F5)


title: Stage E7.0 endoderm single cell plate 3F1 cell (E7.0SCVE3-F1)


title: Stage E7.0 endoderm single cell plate 3G7 cell (E7.0SCVE3-G7)


title: Stage E7.0 endoderm single cell plate 3F10 cell (E7.0SCVE3-F10)


title: Stage E7.0 endoderm single cell plate 3F2 cell (E7.0SCVE3-F2)


title: Stage E7.0 endoderm single cell plate 3F12 cell (E7.0SCVE3-F12)


title: Stage E7.0 endoderm single cell plate 3F3 cell (E7.0SCVE3-F3)


title: Stage E7.0 endoderm single cell plate 3F4 cell (E7.0SCVE3-F4)


title: IP Clone b, 4OHT treated for 2hrs  [H3K27me3]

library_source: genomic

data_processing:
reads were mapped uning bowtie2
duplicate reads were removed
reads were quality filtered
reads were counted using bedtools coverage
Genome_build: mm10

molecule: genomic DNA

source_name: mouse embryonic stem cells stably expressing a cRAF-ErT2 expression cassette

extract_protocol:
Cells we fixed in 1% formaldehyde at RT for 10 minutes, nuclei extracted and chromatin sonicated using a bioruptor (10 cycles, 30s on 30s off). Cleared chromatin was incubated with anti-H3K27me3 antibody (CST 9733). Input DNA serves as negative control for antibody enrichment.
Libraries were prepared using the NEB Next Ultra 2 kit.

treatment_protocol: Cells were left untreated (0h), or treated with 250nM 4OHT (2h).

tag: antibody

value: anti-H3K27me3 antibody


title: Stage E7.0 endoderm single cell plate 3E9 cell (E7.0SCVE3-E9)

tag: cell type


title: 0h_KO clone C -DOX

description:
nascent RNA
0h_KO_C

tag: strain


title: Stage E7.0 endoderm single cell plate 3G6 cell (E7.0SCVE3-G6)


title: Stage E7.0 endoderm single cell plate 3E8 cell (E7.0SCVE3-E8)


title: IP Clone a, 4OHT treated for 2hrs  [H3K27me3]

value: mouse embryonic stem cells stably expressing a cRAF-ErT2 expression cassette


title: IP Clone b, untreated  [H3K27me3]


title: Stage E7.0 endoderm single cell plate 3E7 cell (E7.0SCVE3-E7)


title: Stage E7.0 endoderm single cell plate 3E6 cell (E7.0SCVE3-E6)


title: Stage E7.0 endoderm single cell plate 3G12 cell (E7.0SCVE3-G12)


title: IP Clone a, untreated  [H3K27me3]


title: Stage E7.0 endoderm single cell plate 3E5 cell (E7.0SCVE3-E5)


title: Stage E7.0 endoderm single cell plate 3E3 cell (E7.0SCVE3-E3)


title: Stage E7.0 endoderm single cell plate 3E2 cell (E7.0SCVE3-E2)


title: Input Clone b, 4OHT treated for 2hrs  [H3K27me3]

value: input


title: Input Clone a, 4OHT treated for 2hrs  [H3K27me3]


title: Stage E7.0 endoderm single cell plate 3F8 cell (E7.0SCVE3-F8)


title: Stage E7.0 endoderm single cell plate 3F6 cell (E7.0SCVE3-F6)


title: Stage E7.0 endoderm single cell plate 3E12 cell (E7.0SCVE3-E12)


title: Stage E7.0 endoderm single cell plate 3E1 cell (E7.0SCVE3-E1)


title: Stage E7.0 endoderm single cell plate 3F11 cell (E7.0SCVE3-F11)


title: Input Clone b, untreated  [H3K27me3]


title: Stage E7.0 endoderm single cell plate 3E10 cell (E7.0SCVE3-E10)


title: Stage E7.0 endoderm single cell plate 3E11 cell (E7.0SCVE3-E11)


title: Input Clone a, untreated  [H3K27me3]


title: Stage E7.0 endoderm single cell plate 3D7 cell (E7.0SCVE3-D7)


title: Stage E7.0 endoderm single cell plate 3D9 cell (E7.0SCVE3-D9)


title: Stage E7.0 endoderm single cell plate 3D8 cell (E7.0SCVE3-D8)


title: Stage E7.0 endoderm single cell plate 3D6 cell (E7.0SCVE3-D6)


title: Stage E7.0 endoderm single cell plate 3D2 cell (E7.0SCVE3-D2)


title: Stage E7.0 endoderm single cell plate 3D4 cell (E7.0SCVE3-D4)


title: Stage E7.0 endoderm single cell plate 3D5 cell (E7.0SCVE3-D5)


title: Stage E7.0 endoderm single cell plate 3D3 cell (E7.0SCVE3-D3)


title: Stage E7.0 endoderm single cell plate 3E4 cell (E7.0SCVE3-E4)


title: Stage E7.0 endoderm single cell plate 3D12 cell (E7.0SCVE3-D12)


title: Stage E7.0 endoderm single cell plate 3D10 cell (E7.0SCVE3-D10)


title: Stage E7.0 endoderm single cell plate 3C8 cell (E7.0SCVE3-C8)


title: Stage E7.0 endoderm single cell plate 3D1 cell (E7.0SCVE3-D1)


title: Stage E7.0 endoderm single cell plate 3C7 cell (E7.0SCVE3-C7)


title: Stage E7.0 endoderm single cell plate 3C6 cell (E7.0SCVE3-C6)


title: Stage E7.0 endoderm single cell plate 3C9 cell (E7.0SCVE3-C9)


title: Stage E7.0 endoderm single cell plate 3C5 cell (E7.0SCVE3-C5)


title: Stage E7.0 endoderm single cell plate 3D11 cell (E7.0SCVE3-D11)


title: Stage E7.0 endoderm single cell plate 3C1 cell (E7.0SCVE3-C1)


title: Stage E7.0 endoderm single cell plate 3C3 cell (E7.0SCVE3-C3)


title: Stage E7.0 endoderm single cell plate 3C2 cell (E7.0SCVE3-C2)


title: Stage E7.0 endoderm single cell plate 3B9 cell (E7.0SCVE3-B9)


title: Stage E7.0 endoderm single cell plate 3C10 cell (E7.0SCVE3-C10)


title: Stage E7.0 endoderm single cell plate 3B8 cell (E7.0SCVE3-B8)


title: Stage E7.0 endoderm single cell plate 3B7 cell (E7.0SCVE3-B7)


title: Stage E7.0 endoderm single cell plate 3B5 cell (E7.0SCVE3-B5)


title: Stage E7.0 endoderm single cell plate 3B6 cell (E7.0SCVE3-B6)


title: Stage E7.0 endoderm single cell plate 3B3 cell (E7.0SCVE3-B3)


title: Stage E7.0 endoderm single cell plate 3B4 cell (E7.0SCVE3-B4)


title: Stage E7.0 endoderm single cell plate 3B12 cell (E7.0SCVE3-B12)


title: Stage E7.0 endoderm single cell plate 3B2 cell (E7.0SCVE3-B2)


title: Stage E7.0 endoderm single cell plate 3B11 cell (E7.0SCVE3-B11)


title: Stage E7.0 endoderm single cell plate 3B1 cell (E7.0SCVE3-B1)


title: Stage E7.0 endoderm single cell plate 3A9 cell (E7.0SCVE3-A9)


title: Stage E7.0 endoderm single cell plate 3B10 cell (E7.0SCVE3-B10)


title: Stage E7.0 endoderm single cell plate 3A8 cell (E7.0SCVE3-A8)


title: Stage E7.0 endoderm single cell plate 3C4 cell (E7.0SCVE3-C4)


title: Stage E7.0 endoderm single cell plate 3A7 cell (E7.0SCVE3-A7)


title: Stage E7.0 endoderm single cell plate 3A5 cell (E7.0SCVE3-A5)


title: Stage E7.0 endoderm single cell plate 3A4 cell (E7.0SCVE3-A4)


title: Stage E7.0 endoderm single cell plate 3A2 cell (E7.0SCVE3-A2)


title: Stage E7.0 endoderm single cell plate 3A3 cell (E7.0SCVE3-A3)


title: Stage E7.0 endoderm single cell plate 3C11 cell (E7.0SCVE3-C11)


title: Stage E7.0 endoderm single cell plate 3A12 cell (E7.0SCVE3-A12)


title: Stage E7.0 endoderm single cell plate 3A11 cell (E7.0SCVE3-A11)


title: Stage E7.0 endoderm single cell plate 3A1 cell (E7.0SCVE3-A1)


title: Stage E7.0 endoderm single cell plate 3A10 cell (E7.0SCVE3-A10)


title: Stage E7.0 endoderm single cell plate 2H8 cell (E7.0SCVE2-H8)


title: Stage E7.0 endoderm single cell plate 2H7 cell (E7.0SCVE2-H7)


title: Stage E7.0 endoderm single cell plate 2H9 cell (E7.0SCVE2-H9)


title: Stage E7.0 endoderm single cell plate 2H6 cell (E7.0SCVE2-H6)


title: Stage E7.0 endoderm single cell plate 2H5 cell (E7.0SCVE2-H5)


title: Clone b, PP1 and  4OHT treated for 2hrs

description: nascent RNA

data_processing:
Reads were mapped using STAR, removing multi-mappers
Count tables were generated using featureCounts
Genome_build: mm10

value: PP1 and  4OHT treated for 2hrs

value: Erk1/2 KO ESCS expressing ERK2 Q103A

value: Mouse embryonic stem cells


title: Clone c, PP1 and  4OHT treated for 2hrs

description: nascent RNA

value: embryonic


title: Stage E7.0 endoderm single cell plate 2H4 cell (E7.0SCVE2-H4)


title: Clone a, PP1 and  4OHT treated for 2hrs

description: nascent RNA


title: Stage E7.0 endoderm single cell plate 2H3 cell (E7.0SCVE2-H3)


title: Clone c, PP1

description: nascent RNA


title: Clone b, PP1

description: nascent RNA


title: Clone a, PP1

description: nascent RNA


title: Stage E7.0 endoderm single cell plate 2H2 cell (E7.0SCVE2-H2)


title: Stage E7.0 endoderm single cell plate 3A6 cell (E7.0SCVE3-A6)


title: Stage E7.0 endoderm single cell plate 2H11 cell (E7.0SCVE2-H11)


title: Stage E7.0 endoderm single cell plate 2H12 cell (E7.0SCVE2-H12)


title: Stage E7.0 endoderm single cell plate 2H10 cell (E7.0SCVE2-H10)


title: Stage E7.0 endoderm single cell plate 2G9 cell (E7.0SCVE2-G9)


title: Clone c,MEKi and 4OHT treated for 2hrs

description: nascent RNA

value: Clone c,MEKi and 4OHT treated for 2hrs


title: Stage E7.0 endoderm single cell plate 2G6 cell (E7.0SCVE2-G6)


title: Stage E7.0 endoderm single cell plate 2G7 cell (E7.0SCVE2-G7)


title: Stage E7.0 endoderm single cell plate 2G8 cell (E7.0SCVE2-G8)


title: Clone a, MEKi and 4OHT treated for 2hrs

description: nascent RNA

value: MEKi and 4OHT treated for 2hrs


title: Clone b, MEKi and 4OHT treated for 2hrs

description: nascent RNA


title: Stage E7.0 endoderm single cell plate 2G4 cell (E7.0SCVE2-G4)


title: Stage E7.0 endoderm single cell plate 2G3 cell (E7.0SCVE2-G3)


title: Stage E7.0 endoderm single cell plate 2G2 cell (E7.0SCVE2-G2)


title: Clone c, MEKi

description: nascent RNA

value: MEKi


title: Stage E7.0 endoderm single cell plate 2G12 cell (E7.0SCVE2-G12)


title: Stage E7.0 endoderm single cell plate 2G1 cell (E7.0SCVE2-G1)


title: Clone b, MEKi

description: nascent RNA


title: Stage E7.0 endoderm single cell plate 2G11 cell (E7.0SCVE2-G11)


title: Stage E7.0 endoderm single cell plate 2G10 cell (E7.0SCVE2-G10)


title: Stage E7.0 endoderm single cell plate 2H1 cell (E7.0SCVE2-H1)


title: Clone a, MEKi

description: nascent RNA


title: Stage E7.0 endoderm single cell plate 2F9 cell (E7.0SCVE2-F9)


title: Stage E7.0 endoderm single cell plate 2F7 cell (E7.0SCVE2-F7)


title: Clone b, 4OHT treated for 2hrs  [ERK-AS]

description: nascent RNA

value: 4OHT treated for 2hrs


title: Stage E7.0 endoderm single cell plate 2F6 cell (E7.0SCVE2-F6)


title: Stage E7.0 endoderm single cell plate 2F8 cell (E7.0SCVE2-F8)


title: Clone c, 4OHT treated for 2hrs  [ERK-AS]

description: nascent RNA


title: Stage E7.0 endoderm single cell plate 2F5 cell (E7.0SCVE2-F5)


title: Clone a, 4OHT treated for 2hrs  [ERK-AS]

description: nascent RNA


title: Stage E7.0 endoderm single cell plate 2F3 cell (E7.0SCVE2-F3)


title: Stage E7.0 endoderm single cell plate 2F4 cell (E7.0SCVE2-F4)


title: Stage E7.0 endoderm single cell plate 2F2 cell (E7.0SCVE2-F2)


title: Stage E7.0 endoderm single cell plate 2G5 cell (E7.0SCVE2-G5)


title: Clone c, DMSO

description: nascent RNA

value: DMSO


title: Stage E7.0 endoderm single cell plate 2F1 cell (E7.0SCVE2-F1)

value: Mid-gastrulation embryo (E7.0)


title: Stage E7.0 endoderm single cell plate 2F12 cell (E7.0SCVE2-F12)

value: Mouse embryonic cells


title: Stage E7.0 endoderm single cell plate 2F11 cell (E7.0SCVE2-F11)


title: Clone b, DMSO

description: nascent RNA


title: Stage E7.0 endoderm single cell plate 2F10 cell (E7.0SCVE2-F10)


title: ribosome profiling APP/PSEN1_3

city: Zurich

first: Claudia

last: Scheckel

state: NY

address: Schmelzbergstrasse 12

department: Institute of Neuropathology

country: Switzerland

institute: University Hospital Zurich

data_processing:
filtering (min:0-13:20,mean:14-39:20)
remove 3'linker with cutadapt (GTGTCAGTCACTTCCAGCGG)
collapse exact duplicates
remove 5'linker (first 14 nucleotides)
alignment with STAR allowing only 1 mismatch
Genome_build: hg19
Supplementary_files_format_and_content: combined ReadsPerGene STAR output files (containing uniquely aligned reads per gene)

source_name: APP/PSEN1 double mutant iPSC-derived neurons

growth_protocol: induction and maturation of cortical neurons from iPS cells (total of 80 days in vitro; detailed protocol in accompanying paper)

extract_protocol:
cell lysis and partial RNAse digestion followed by ribosome immunoprecipitation to extract ribosome associated fragments (detailed protocol in accompanying paper)
partial RNAse digestion, ribosome associated fragment purification, linker ligation, reverse transcription, cDNA purification, PCR amplification (detailed protocol in accompanying paper)
ligation of 3' linker, addition of 5'linker with barcode and UMI via RT (detailed protocol in accompanying paper)

tag: cell line background

value: 7889SA parental cell line

tag: cell line source

value: 80 day old cortical neurons

value: co-isogenic iPS cells

tag: mutation

value: APP Swe/Swe; PSEN1 M146V/M146V


title: Stage E7.0 endoderm single cell plate 2E9 cell (E7.0SCVE2-E9)

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

tag: developmental stage

tag: tag


title: Stage E7.0 endoderm single cell plate 2E8 cell (E7.0SCVE2-E8)


title: ribosome profiling APP/PSEN1_1


title: ribosome profiling PSEN_3

source_name: PSEN1 mutant iPSC-derived neurons

value: PSEN1 M146V/M146V


title: Stage E7.0 endoderm single cell plate 2E6 cell (E7.0SCVE2-E6)


title: Stage E7.0 endoderm single cell plate 2E5 cell (E7.0SCVE2-E5)


title: Stage E7.0 endoderm single cell plate 2E3 cell (E7.0SCVE2-E3)


title: ribosome profiling PSEN_2


title: Stage E7.0 endoderm single cell plate 2E4 cell (E7.0SCVE2-E4)


title: Stage E7.0 endoderm single cell plate 2E2 cell (E7.0SCVE2-E2)


title: Stage E7.0 endoderm single cell plate 2E1 cell (E7.0SCVE2-E1)


title: Stage E7.0 endoderm single cell plate 2E11 cell (E7.0SCVE2-E11)


title: Stage E7.0 endoderm single cell plate 2E10 cell (E7.0SCVE2-E10)


title: ribosome profiling PSEN_1


title: Stage E7.0 endoderm single cell plate 2D7 cell (E7.0SCVE2-D7)


title: ribosome profiling APP_2

source_name: APP mutant iPSC-derived neurons

value: APP Swe/Swe


title: ribosome profiling APP_3


title: Stage E7.0 endoderm single cell plate 2D9 cell (E7.0SCVE2-D9)


title: Stage E7.0 endoderm single cell plate 2D8 cell (E7.0SCVE2-D8)


title: Stage E7.0 endoderm single cell plate 2E12 cell (E7.0SCVE2-E12)


title: Stage E7.0 endoderm single cell plate 2D6 cell (E7.0SCVE2-D6)


title: ribosome profiling APP_1


title: ribosome profiling wt_3

source_name: wiltype iPSC-derived neurons


title: Stage E7.0 endoderm single cell plate 2D5 cell (E7.0SCVE2-D5)


title: 2h_B

data_processing:
reads were mapped uning bowtie2
duplicate reads were removed
reads were quality filtered
reads were counted using bedtools coverage
peaks were called using MACS2 (broad)
Genome_build: mm10

extract_protocol:
Nuclei were purified by incubation with 10mM TrisHCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.3% Igepal. Open DNA was tagged using the tn5 transposase kit (Illumina)
Fragments were indexed and amplidied using standard Illumina barcodes

treatment_protocol: Cells were left untreated (0h), or treated with 250nM 4OHT (1h, 2h).

value: mouse embryonic stem cells stably expressing a cRAF-ErT2 expression cassette

value: 2h 4OHT


title: Stage E7.0 endoderm single cell plate 2D4 cell (E7.0SCVE2-D4)

data_processing:
The reads for all samples are mapped to the mm10 using Tophat v2.0.8b with parameter: -p 20 -g 1 -N 4 --read-edit-dist 4 --microexon-search
The mapped reads were used to estimate transcriptomic alignment rates, and were also used as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each embryo


title: Stage E7.0 endoderm single cell plate 2D3 cell (E7.0SCVE2-D3)


title: Stage E7.0 endoderm single cell plate 2E7 cell (E7.0SCVE2-E7)


title: ribosome profiling APP/PSEN1_2


title: 2h_A


title: Stage E7.0 endoderm single cell plate 2D12 cell (E7.0SCVE2-D12)


title: ribosome profiling wt_1


title: Stage E7.0 endoderm single cell plate 2D1 cell (E7.0SCVE2-D1)


title: 1h_C

value: 1h 4OHT


title: Stage E7.0 endoderm single cell plate 2D11 cell (E7.0SCVE2-D11)


title: ribosome profiling wt_2


title: Stage E7.0 endoderm single cell plate 3C12 cell (E7.0SCVE3-C12)


title: RNAseq APP/PSEN1_3 [1233]

data_processing:
alignment with STAR (default mode)
Genome_build: hg19
Supplementary_files_format_and_content: combined ReadsPerGene STAR output files (containing uniquely aligned reads per gene)

extract_protocol:
Trizol extraction, rRNA removal via Ribo-Zero treatment, DNAse-digestion
Illumina High-Throughput TruSeq


title: Stage E7.0 endoderm single cell plate 2C9 cell (E7.0SCVE2-C9)


title: Stage E7.0 endoderm single cell plate 2D10 cell (E7.0SCVE2-D10)


title: RNAseq APP/PSEN1_2 [1232]


title: Stage E7.0 endoderm single cell plate 2C7 cell (E7.0SCVE2-C7)


title: Stage E7.0 endoderm single cell plate 2C8 cell (E7.0SCVE2-C8)


title: 1h_A

value: embryonic


title: 2h_C


title: RNAseq APP/PSEN1_1 [1231]


title: 0h_C

value: 0h 4OHT


title: RNAseq PSEN_3 [1230]


title: Stage E7.0 endoderm single cell plate 2C6 cell (E7.0SCVE2-C6)


title: RNAseq PSEN_2 [1229]


title: 0h_B


title: Stage E7.0 endoderm single cell plate 2C5 cell (E7.0SCVE2-C5)


title: Stage E7.0 endoderm single cell plate 2C4 cell (E7.0SCVE2-C4)


title: Stage E7.0 endoderm single cell plate 2D2 cell (E7.0SCVE2-D2)


title: Stage E7.0 endoderm single cell plate 2C2 cell (E7.0SCVE2-C2)


title: 0h_A


title: Stage E7.0 endoderm single cell plate 2C3 cell (E7.0SCVE2-C3)


title: Stage E7.0 endoderm single cell plate 2C1 cell (E7.0SCVE2-C1)


title: Clone c, 4OHT treated for 2hrs

description:
nascent RNA
C_2h


title: Clone b, 4OHT treated for 2hrs

description:
nascent RNA
B_2h


title: RNAseq APP_3 [1227]


title: RNAseq PSEN_1 [1228]


title: Stage E7.0 endoderm single cell plate 2C10 cell (E7.0SCVE2-C10)


title: Stage E7.0 endoderm single cell plate 2C11 cell (E7.0SCVE2-C11)


title: Stage E7.0 endoderm single cell plate 2C12 cell (E7.0SCVE2-C12)


title: Stage E7.0 endoderm single cell plate 2B9 cell (E7.0SCVE2-B9)


title: RNAseq APP_2 [1226]


title: Clone a, 4OHT treated for 2hrs

description:
nascent RNA
A_2h


title: Stage E7.0 endoderm single cell plate 2B8 cell (E7.0SCVE2-B8)


title: Stage E7.0 endoderm single cell plate 2B7 cell (E7.0SCVE2-B7)


title: RNAseq APP_1 [1225]


title: Stage E7.0 endoderm single cell plate 2B5 cell (E7.0SCVE2-B5)


title: Stage E7.0 endoderm single cell plate 2B6 cell (E7.0SCVE2-B6)


title: RNAseq wt_3 [1224]


title: Clone b, untreated

description:
nascent RNA
B_0h

value: untreated


title: Stage E7.0 endoderm single cell plate 2B4 cell (E7.0SCVE2-B4)


title: Stage E7.0 endoderm single cell plate 2B2 cell (E7.0SCVE2-B2)


title: RNAseq wt_2 [1223]


title: Clone a, untreated

description:
nascent RNA
A_0h


title: Stage E7.0 endoderm single cell plate 2B3 cell (E7.0SCVE2-B3)


title: Stage E7.0 endoderm single cell plate 2B11 cell (E7.0SCVE2-B11)


title: Stage E7.0 endoderm single cell plate 2B1 cell (E7.0SCVE2-B1)


title: Stage E7.0 endoderm single cell plate 2B12 cell (E7.0SCVE2-B12)


title: Stage E7.0 endoderm single cell plate 2B10 cell (E7.0SCVE2-B10)


title: RNAseq wt_1 [1222]


title: RNAseq of 293TL tumor line

city: Chicago

first: Yingtao

last: Bi

state: IL

address: 750 North Lake shore drive

institute: Northwestern University

data_processing:
FastQC was applied on raw fastq files to examine the sequence quality
Tophat  was used for tag alignment
Counts for each gene were computed by means of HTSeq Python package using the annotation of the Ensembl genes and only reads that mapped to exons
Genome_build: hg19
Supplementary_files_format_and_content: Counts of sequenced reads for each gene

source_name: tumor line

growth_protocol: Transplantations of RG cells to the SVZ of 3rd ventricle of the brain of NOD-SCID mice

extract_protocol:
Total RNA isolation from tumor tissues was performed with the PureZOL RNA isolation reagnet, followed by DNAse treatment
Library making protocol guide for RiboZero selection was used followed by sequencing using Illumina HiSeq2500

tag: tumor line

value: 293TL tumor line


title: 8h clone b IP

description: ChIP-seq

data_processing:
reads were mapped uning bowtie2
duplicate reads were removed
reads were quality filtered
reads were counted using bedtools coverage
Genome_build: mm10
Supplementary_files_format_and_content: excel file

extract_protocol:
Cells we fixed in 1% formaldehyde at RT for 10 minutes, nuclei extracted and chromatin sonicated using a bioruptor (10 cycles, 30s on 30s off). Cleared chromatin was incubated with anti-RBP1 antibody (Active Motif, 39097). Input DNA serves as negative control for antibody enrichment.
Libraries were prepared using the NEB Next Ultra 2 kit.

treatment_protocol: Cells were left untreated (0h), or treated with 250nM 4OHT (2h, 8h), or treated with 4OHT for 8hrs followed by a subsequent 2h Mek inhibitor treatment (8_2h).

value: 8h with 4OHT

tag: cell line

tag: chip antibody

value: anti-RBP1 (Active Motif, 39097)


title: 8h clone a IP

description: ChIP-seq

tag: treatment


title: 8h clone c IP

description: ChIP-seq


title: RNAseq of 170TL tumor line

value: 170TL tumor line


title: RNAseq of 138TL tumor line

value: 138TL tumor line


title: Clone c, untreated

description:
nascent RNA
C_0h


title: Stage E7.0 endoderm single cell plate 2A8 cell (E7.0SCVE2-A8)

value: Mid-gastrulation embryo (E7.0)

value: Mouse embryonic cells


title: 8h-2h Meki clone c IP

description: ChIP-seq

value: 8h with 4OHT plus 2 hours with MEK inhibitor PD0325901


title: 1h_B


title: RNAseq of LCAS-R Radial glia cell line

source_name: Radial glia cell line

value: LCAS-R Radial glia cell line

tag: protocol

value: transplantation of RG cells to SVZ of 3rd ventricle of brain of NOD-SCID mice


title: Stage E7.0 endoderm single cell plate 2A6 cell (E7.0SCVE2-A6)


title: RNAseq of CM14-R Radial glia cell line

value: CM14-R Radial glia cell line


title: Stage E7.0 endoderm single cell plate 2A3 cell (E7.0SCVE2-A3)


title: Stage E7.0 endoderm single cell plate 2A4 cell (E7.0SCVE2-A4)


title: Stage E7.0 endoderm single cell plate 2A2 cell (E7.0SCVE2-A2)


title: Stage E7.0 endoderm single cell plate 2A1 cell (E7.0SCVE2-A1)


title: 8h-2h Meki clone b IP

description: ChIP-seq


title: 2h clone c IP

description: ChIP-seq

value: 2h with 4OHT


title: 2h clone b IP

description: ChIP-seq


title: Stage E7.0 endoderm single cell plate 2A11 cell (E7.0SCVE2-A11)


title: Stage E7.0 endoderm single cell plate 2A10 cell (E7.0SCVE2-A10)


title: 2h clone a IP

description: ChIP-seq


title: Stage E7.0 endoderm single cell plate 2A9 cell (E7.0SCVE2-A9)


title: Stage E7.0 endoderm single cell plate 1H9 cell (E7.0SCVE1-H9)


title: Stage E7.0 endoderm single cell plate 2A7 cell (E7.0SCVE2-A7)


title: Stage E7.0 endoderm single cell plate 1H8 cell (E7.0SCVE1-H8)


title: RNAseq of LC25-R Radial glia cell line

value: LC25-R Radial glia cell line


title: Sample 44: wt control 250 lumbar

data_processing:
FASTQ files were filtered for reads with a minimum average base quality greater than or equal to 15 and known Illumina adapters were trimmed using tools from the BBMap package.
Isoform expression was quantified with kallisto and the M17 gencode annotation for the mm10 mouse genome.
Isoform expressions were summed into gene level expression based on gencode gene id.
Genome_build: mm10
Supplementary_files_format_and_content: gene level unnormalized counts are provided for all samples in a CSV format file

source_name: spinal cord (lumbar)

extract_protocol:
Qiagen RNeasy Plus Mini kit was used to extract RNA from flash frozen cervical and lumbar spinal cords.  RNA was extracted following manufacturer's protocol.  RNA quality was assayed using Agilent Tapestation analysis.
Illumina TruSeq stranded mRNA kit, following by single-end 75bp sequencing on Illumina HiSeq4000 machine.

treatment_protocol: SOD1 G37R mice were treated with shRNA-SOD1 at either ~120d (presymptomatic) or ~348d (mid-onset disease).  End-stage control animals were ~390d at the time of tissue harvesting, whereas shRNA-treated animals treated presymptomatically were ~470d at the time of tissue harvesting.  shRNA-treated animals that were treated after disease onset survived for three additional months after treatment without progression of disease before tissue harvesting.

tag: tissue

value: spinal cord (lumbar)

tag: sequencing batch

value: Batch 2

tag: age euthanized (days)

tag: genotype

value: Wild Type


title: Stage E7.0 endoderm single cell plate 1H7 cell (E7.0SCVE1-H7)


title: Stage E7.0 endoderm single cell plate 1H6 cell (E7.0SCVE1-H6)


title: Stage E7.0 endoderm single cell plate 2A5 cell (E7.0SCVE2-A5)


title: Sample 43: wt control 250 cervical

source_name: spinal cord (cervical)

value: spinal cord (cervical)


title: Stage E7.0 endoderm single cell plate 1H5 cell (E7.0SCVE1-H5)


title: 0h clone b IP

description: ChIP-seq

value: 0h with 4OHT

tag: background strain

tag: Stage

value: embryonic


title: Sample 42: untreated SOD1 844 lumbar

value: SOD1 G37R


title: 0h clone c IP

description: ChIP-seq

value: anti-RBP1 (Active Motif, 39097)


title: 0h clone a IP

description: ChIP-seq


title: Stage E7.0 endoderm single cell plate 1H4 cell (E7.0SCVE1-H4)

tag: cell type


title: Stage E7.0 endoderm single cell plate 1H2 cell (E7.0SCVE1-H2)


title: Stage E7.0 endoderm single cell plate 1H3 cell (E7.0SCVE1-H3)


title: 8h clone c input for RBP1 ChIP

description: ChIP-seq

value: 8h with 4OHT

value: none (input)


title: RNAseq of LC26-R Radial glia cell line

value: LC26-R Radial glia cell line


title: Sample 41: untreated SOD1 844 cervical


title: Stage E7.0 endoderm single cell plate 1H1 cell (E7.0SCVE1-H1)

value: Mid-gastrulation embryo (E7.0)

value: Mouse embryonic cells


title: 8h clone b input for RBP1 ChIP

description: ChIP-seq


title: Stage E7.0 endoderm single cell plate 2A12 cell (E7.0SCVE2-A12)


title: Sample 40: untreated SOD1 836 lumbar


title: Stage E7.0 endoderm single cell plate 1H11 cell (E7.0SCVE1-H11)


title: Stage E7.0 endoderm single cell plate 1H12 cell (E7.0SCVE1-H12)


title: Sample 39: untreated SOD1 836 cervical


title: Stage E7.0 endoderm single cell plate 1H10 cell (E7.0SCVE1-H10)


title: 8h clone a input for RBP1 ChIP

description: ChIP-seq


title: Sample 38: untreated SOD1 834 lumbar


title: Stage E7.0 endoderm single cell plate 1G9 cell (E7.0SCVE1-G9)


title: Stage E7.0 endoderm single cell plate 1G8 cell (E7.0SCVE1-G8)


title: Stage E7.0 endoderm single cell plate 1G7 cell (E7.0SCVE1-G7)


title: 8h-2h Meki clone b input for RBP1 ChIP

description: ChIP-seq

value: 8h with 4OHT plus 2 hours with MEK inhibitor PD0325901


title: Stage E7.0 endoderm single cell plate 1G6 cell (E7.0SCVE1-G6)


title: Stage E7.0 endoderm single cell plate 1G5 cell (E7.0SCVE1-G5)


title: Sample 37: untreated SOD1 834 cervical


title: Stage E7.0 endoderm single cell plate 1G3 cell (E7.0SCVE1-G3)


title: Sample 36: Tx shRNA SOD1 254 lumbar

value: shRNA-SOD1 at 348d


title: Stage E7.0 endoderm single cell plate 1G4 cell (E7.0SCVE1-G4)


title: Stage E7.0 endoderm single cell plate 1G2 cell (E7.0SCVE1-G2)


title: 2h clone c input for RBP1 ChIP

description: ChIP-seq

value: 2h with 4OHT


title: 2h clone b input for RBP1 ChIP

description: ChIP-seq


title: Stage E7.0 endoderm single cell plate 1G1 cell (E7.0SCVE1-G1)


title: Stage E7.0 endoderm single cell plate 1G12 cell (E7.0SCVE1-G12)


title: Stage E7.0 endoderm single cell plate 1G11 cell (E7.0SCVE1-G11)


title: Sample 34: Tx shRNA SOD1 234 lumbar


title: 2h clone a input for RBP1 ChIP

description: ChIP-seq


title: 0h clone c input for RBP1 ChIP

description: ChIP-seq


title: 0h clone b input for RBP1 ChIP

description: ChIP-seq


title: Myc BDR3 rep2

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

data_processing:
Trimming: Trimmomatic (v0.38, Bolger, Lohse & Usabel, Bioinformatics, 2014 ; btu170) in paired end mode
Alignment: Bowtie2 (v 2.3.4.1, Langmead & Salzberg, Nature Methods, 2012 ; 9:357-59) with—very-sensitive and --dovetail option and a maximum insert size of 1Kb
Filtering: Duplicate reads were identified with Picard (v. 2.18.2) MarkDuplicates and removed. Samtools v 1.8 was used to keep only reads mapped in proper pairs with mapping quality (MapQ) above 2.
Coverage and normalization: Aligned reads were imported in R (v.3.4.3) to obtain coverages using Bioconductor (v3.6). Coverages were normalized as fragments per million (FPM) and exported to bigWig files with the rtracklayer package.
Peak calling: ChIP-seq peaks for BDR3 were detected from Myc_BDR3_rep2 using MACS2 (v. 2.1.1, Zhang et al., Genome Biology, 2008 ; 9:R137) in paired-end mode and Myc_WT as controls. peaks with a p-value<0.01 were kept. Peaks located in blacklisted regions were removed.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files contain the normalized coverage (FPM: fragments per million), i.e. the normalized number of fragments covering each base
Supplementary_files_format_and_content: bed files contain the location of BDR3 peaks or peak summits identified with MACS2

source_name: seedlings, 8-day-old

growth_protocol: Seeds were sown on MS plates and stratified for 4 days at 4°C in the dark. Plates were transfered to a growth chamber at 21°C and grown for 8 days under long day conditions (16h light/8h dark).

extract_protocol:
The seedlings were crosslinked for 15 min in 1 % formaldehyde under vacuum (5 min vacuum / vacuum release / 10 min vacuum) followed by 6 min quenching with glycine (125mM final concentration, under vacuum), extensive rinsing with ice-cold water and drying. Crosslinked seedlings were ground into fine powder in liquid nitrogen, incubated for 15 min at 4°C in extraction buffer (25mM Tris-HCl, pH=8.0, 0.44M sucrose, 10mM MgCl2, 0.1 % Triton X-100, 2mM spermine, 10mM beta-mercaptoethanol, 1 mM PMSF, 1 % plant protease inhibitor cocktail) and filtered through 2 layers of Miracloth. Nuclei were prepared by 3 rounds of resuspension in extraction buffer (without spermine, twice with 0.25 % Triton X-100 and once with 0.1 % Triton X-100), incubation 12 min on ice and centrifugation at 1,000g for 12 min at 4°C (only 300g for the last centrifugation). The nuclei suspension was stored in 20 % glycerol at -70°C until used. After thawing on ice, nuclei were centrifuged for 10 min at 11,000g at 4°C and resuspended in nuclei lysis buffer (500 mM Tris-HCl, pH=8.0, 10mM EDTA, 1 % SDS, 1mM PMSF, 1 % plant protease inhibitor cocktail). Chromatin was sonicated for 12 min using a Covaris S220 (peak power=150, duty factor=20, cycles/burst=200). Soluble chromatin was recovered by centrifugation at 13,000g for 15 min at 4°C and diluted to (final concentrations): 20mM Tris-HCl, 150mM NaCl, 2mM EDTA, 0.1 % SDS, 1 % Triton X-100, 1mM PMSF, 1 % plant protease inhibitor cocktail.
Libraries were prepared using NEBNext Ultra II DNA library prep kits (NEB E7645). Libraries were sequenced on a NextSeq 500 instrument at Indiana University Center for Genomics and Bioinformatics.

value: seedlings

tag: ecotype

value: bdrs expressing Myc tag-BDR3

tag: lineid

tag: age

value: 8-day old

value: Anti-Myc tag, clone 4A6 (Millipore 05-724, lot 2824030)

tag: library prep kit

value: NEBNext Ultra II DNA library Prep kit (E7645)


title: 8h-2h Meki clone c input for RBP1 ChIP

description: ChIP-seq


title: Stage E7.0 endoderm single cell plate 1F8 cell (E7.0SCVE1-F8)

tag: developmental stage

tag: tag


title: 0h clone a input for RBP1 ChIP

description: ChIP-seq

value: 0h with 4OHT

tag: cell line


title: Myc BDR3 rep1

tag: chip antibody


title: Sample 30: untreated SOD1 215 lumbar

value: spinal cord (lumbar)

value: Batch 1

tag: treatment


title: Stage E7.0 endoderm single cell plate 1F7 cell (E7.0SCVE1-F7)


title: Sample 35: Tx shRNA SOD1 254 cervical

value: spinal cord (cervical)

value: Batch 2

value: SOD1 G37R


title: Myc BDR1

value: bdrs expressing Myc tag-BDR1


title: Stage E7.0 endoderm single cell plate 1F6 cell (E7.0SCVE1-F6)

value: Mid-gastrulation embryo (E7.0)


title: Sample 29: untreated SOD1 215 cervical


title: Myc WT

value: wild-type


title: Stage E7.0 endoderm single cell plate 1F4 cell (E7.0SCVE1-F4)

value: Mouse embryonic cells


title: Sample 28: untreated SOD1 212 lumbar


title: Sample 27: untreated SOD1 212 cervical


title: Sample 33: Tx shRNA SOD1 234 cervical

value: shRNA-SOD1 at 348d


title: RNAPII_WT_rep3

data_processing:
Trimming : Trimmomatic (v0.33, Bolger, Lohse & Usabel, Bioinformatics, 2014 ; btu170) in paired end mode
Alignment : Bowtie2 (v 2.2.6, Langmead & Salzberg, Nature Methods, 2012 ; 9:357-59) with --dovetail option and a maximum insert size of 1Kb
Filtering : Duplicate reads were identified with Picard (v. 2.2.4) MarkDuplicates and removed. Samtools v 1.3 was used to keep only reads mapped in proper pairs with mapping quality (MapQ) above 2.
Coverage and normalization: Aligned reads were imported in R (v.3.3.2) to obtain coverages using Bioconductor (v3.4). Coverages were normalized as fragments per 10 million (FP10M) and exported to bigWig files with the rtracklayer package.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files contain the normalized coverage (FP10M : fragments per 10 million), i.e. the normalized number of fragments covering each base

source_name: seedlings, 7-day-old

growth_protocol: Seeds were sown on MS plates and stratified for 4 days at 4°C in the dark. Plates were transfered to a growth chamber at 21°C and grown for 7 or 8 days under long day conditions (16h light/8h dark).

extract_protocol:
The seedlings were crosslinked for 15 min in 1 % formaldehyde under vacuum (5 min vacuum / vacuum release / 10 min vacuum) followed by 6 min quenching with glycine (125mM final concentration, under vacuum), extensive rinsing with ice-cold water and drying. Crosslinked seedlings were ground into fine powder in liquid nitrogen, incubated for 15 min at 4°C in extraction buffer (25mM Tris-HCl, pH=8.0, 0.44M sucrose, 10mM MgCl2, 0.1 % Triton X-100, 2mM spermine, 10mM beta-mercaptoethanol, 1 mM PMSF, 1 % plant protease inhibitor cocktail) and filtered through 2 layers of Miracloth. Nuclei were prepared by 3 rounds of resuspension in extraction buffer (without spermine, twice with 0.25 % Triton X-100 and once with 0.1 % Triton X-100), incubation 12 min on ice and centrifugation at 1,000g for 12 min at 4°C (only 300g for the last centrifugation). The nuclei suspension was stored in 20 % glycerol at -70°C until used. After thawing on ice, nuclei were centrifuged for 10 min at 11,000g at 4°C and resuspended in nuclei lysis buffer (500 mM Tris-HCl, pH=8.0, 10mM EDTA, 1 % SDS, 1mM PMSF, 1 % plant protease inhibitor cocktail). Chromatin was sonicated for 12 min using a Covaris S220 (peak power=150, duty factor=20, cycles/burst=200). Soluble chromatin was recovered by centrifugation at 13,000g for 15 min at 4°C and diluted to (final concentrations): 20mM Tris-HCl, 150mM NaCl, 2mM EDTA, 0.1 % SDS, 1 % Triton X-100, 1mM PMSF, 1 % plant protease inhibitor cocktail.
Libraries were prepared using NEBNext Ultra DNA library prep kits (NEB, E7370 or E7645 as indicated). Libraries were sequenced on a NextSeq 500 instrument at Indiana University Center for Genomics and Bioinformatics.

value: 7-day old

value: anti-RNAPII (abcam ab817, lot GR261055-1)

value: NEBNext Ultra DNA library Prep kit (E7370)


title: Stage E7.0 endoderm single cell plate 1G10 cell (E7.0SCVE1-G10)


title: input_WT_rep3


title: Sample 26: untreated SOD1 205 lumbar


title: Stage E7.0 endoderm single cell plate 1F9 cell (E7.0SCVE1-F9)


title: Stage E7.0 endoderm single cell plate 1F3 cell (E7.0SCVE1-F3)


title: Sample 25: untreated SOD1 205 cervical


title: IgG_WT_rep3

value: Control IgG (abcam ab18413, lot GR249563-7)


title: input_fpa_lib2

description: same DNA sample as input_fpa_lib1. Independent library preparation and sequencing run.

value: fpa single mutant (fpa-7)


title: Sample 32: Tx shRNA SOD1 232 lumbar


title: Sample 31: Tx shRNA SOD1 232 cervical


title: Sample 24: sham Tx SOD1 180 lumbar

value: sham injection at 120d


title: input_bdrs_rep1_lib2

description: same DNA sample as input_bdrs_rep1_lib1. Independent library preparation and sequencing run.

value: bdrs triple mutant


title: Sample 23: sham Tx SOD1 180 cervical


title: input_WT_rep1_lib2

description: same DNA sample as input_WT_rep1_lib1. Independent library preparation and sequencing run.


title: Sample 22: sham Tx SOD1 199 lumbar

value: spinal cord (lumbar)


title: Stage E7.0 endoderm single cell plate 1F1 cell (E7.0SCVE1-F1)


title: RNAPII_bdrs_rep2_seq2

description: sequencing replicate of RNAPII_bdrs_rep2_seq1

value: 8-day old

value: anti-RNAPII (abcam ab817, lot GR299078-3)

value: NEBNext Ultra II DNA library Prep kit (E7645)


title: Stage E7.0 endoderm single cell plate 1F5 cell (E7.0SCVE1-F5)


title: RNAPII_WT_rep2_seq2

description: sequencing replicate of RNAPII_WT_rep2_seq1


title: Stage E7.0 endoderm single cell plate 1E9 cell (E7.0SCVE1-E9)


title: Sample 20: sham Tx SOD1 178 lumbar

value: Batch 1

value: SOD1 G37R


title: Sample 21: sham Tx SOD1 199 cervical

value: spinal cord (cervical)


title: S5P_bdrs_rep2

value: anti-Se5P (abcam ab5131, lot GR278215-1)


title: Stage E7.0 endoderm single cell plate 1E8 cell (E7.0SCVE1-E8)

value: Mid-gastrulation embryo (E7.0)

value: Mouse embryonic cells


title: Stage E7.0 endoderm single cell plate 1F2 cell (E7.0SCVE1-F2)


title: Sample 19: sham Tx SOD1 178 cervical


title: S5P_WT_rep2

value: wild-type


title: Sample 18: sham Tx SOD1 155 lumbar


title: Stage E7.0 endoderm single cell plate 1E7 cell (E7.0SCVE1-E7)


title: Stage E7.0 endoderm single cell plate 1E5 cell (E7.0SCVE1-E5)


title: S2P_bdrs_rep2

value: anti-Ser2P (abcam ab5095, lot GR295145-1)


title: Stage E7.0 endoderm single cell plate 1F12 cell (E7.0SCVE1-F12)


title: Sample 17: sham Tx SOD1 155 cervical


title: Stage E7.0 endoderm single cell plate 1E6 cell (E7.0SCVE1-E6)


title: IP Clone b, 4OHT treated for 2hrs

description: ChIP-seq

data_processing:
reads were mapped uning bowtie2
duplicate reads were removed
reads were quality filtered
reads were counted using bedtools coverage
peaks were called using MACS2 (narrow)
Genome_build: mm10
Supplementary_files_format_and_content: MACS PEAK BED

extract_protocol:
Cells we fixed in 1% formaldehyde at RT for 10 minutes, nuclei extracted and chromatin sonicated using a bioruptor (10 cycles, 30s on 30s off). Cleared chromatin was incubated with anti-H3K27ac  antibody (Abcam, ab4729). Input DNA serves as negative control for antibody enrichment.
Libraries were prepared using the NEB Next Ultra 2 kit.

value: 4OHT treated for 2hrs

value: embryonic

value: anti-H3K27ac  (Abcam, ab4729)


title: Sample 16: Tx shRNA SOD1 185 lumbar

value: shRNA-SOD1 at 120d


title: IP Clone a, 4OHT treated for 2hrs

description: ChIP-seq


title: Stage E7.0 endoderm single cell plate 1E4 cell (E7.0SCVE1-E4)


title: Stage E7.0 endoderm single cell plate 1F10 cell (E7.0SCVE1-F10)


title: Sample 15: Tx shRNA SOD1 185 cervical


title: Stage E7.0 endoderm single cell plate 1F11 cell (E7.0SCVE1-F11)


title: IP Clone a, untreated

description: ChIP-seq

value: untreated


title: IP Clone b, untreated

description: ChIP-seq


title: RNAPII_WT_rep2_seq1


title: Sample 14: Tx shRNA SOD1 200 lumbar

value: spinal cord (lumbar)


title: RNAPII_bdrs_rep2_seq1

value: bdrs triple mutant

value: 8-day old


title: Input Clone b, 4OHT treated for 2hrs

description: ChIP-seq

value: none (input)


title: Stage E7.0 endoderm single cell plate 1E3 cell (E7.0SCVE1-E3)


title: Sample 13: Tx shRNA SOD1 200 cervical

value: Batch 1


title: input_bdrs_rep1_lib1

value: 7-day old

value: NEBNext Ultra DNA library Prep kit (E7370)


title: Input Clone a, 4OHT treated for 2hrs

description: ChIP-seq


title: Stage E7.0 endoderm single cell plate 1E1 cell (E7.0SCVE1-E1)


title: input_WT_rep1_lib1


title: input_fpa_lib1

value: fpa single mutant (fpa-7)


title: Stage E7.0 endoderm single cell plate 1E12 cell (E7.0SCVE1-E12)

value: Mid-gastrulation embryo (E7.0)


title: S2P_WT_rep2

value: NEBNext Ultra II DNA library Prep kit (E7645)


title: Input Clone b, untreated

description: ChIP-seq


title: Sample 12: Tx shRNA SOD1 179 lumbar

value: SOD1 G37R


title: Input Clone a, untreated

description: ChIP-seq


title: Sample 11: Tx shRNA SOD1 179 cervical

value: spinal cord (cervical)


title: Stage E7.0 endoderm single cell plate 1E11 cell (E7.0SCVE1-E11)

value: Mouse embryonic cells


title: Stage E7.0 endoderm single cell plate 1E10 cell (E7.0SCVE1-E10)


title: Sample 10: Tx shRNA SOD1 154 lumbar


title: Sample 9: Tx shRNA SOD1 154 cervical


title: S5P_fpa

value: anti-Se5P (abcam ab5131, lot GR118198-2)


title: S5P_bdrs_rep1


title: Lin-CD45-Cd71- Bone-associated fraction

data_processing:
Second read was trimmed to 58 bases; perl
CellRanger 2.0.0, 10x genomics, Pleasanton, CA
Filtering of cells with less than 500 genes observed or more than 5% of molecules stemming from mitochondrial RNA. R-3.5.0, Seurat-2.3.3
R1 = barcode (basepairs 1-16) and UMI (basepairs 17-26)
R2 = biological read
Genome_build: mm10, cellranger version 1.2.0
Supplementary_files_format_and_content: Comma-separated value files of molecule (UMI) counts containing cells (post-filtering) in columns and genes in rows

source_name: Bone chips

extract_protocol:
Fresh bone marrow cells were isolated by crushing mouse bones in media supplemented with FCS. Bone chips were then enzymatically digested using collagenase I and dispase. Cells were stained with fluorescently labelled antibodies against lineage markers (CD4, CD8, CD11b, B220, Gr1, Ter119), CD71 and CD45. A DNA dye was used to exclude debris. Single Lin-CD45-CD71-DNA+ cells were sorted into PBS-2%FCS. Full-length cDNA from individual cells were produced following the Chromium Single Cell 3’ Reagent v2 protocol (10x genomics, Pleasanton, CA) according to manufacturer’s recommendations.
Default library production protocol, 10x genomics, Pleasanton, CA

tag: strain

tag: bm isolation

value: Bone crushing, bone chips

tag: digestion

value: Yes


title: S5P_WT_rep1

value: wild-type


title: Stage E7.0 endoderm single cell plate 1D9 cell (E7.0SCVE1-D9)


title: Stage E7.0 endoderm single cell plate 1D8 cell (E7.0SCVE1-D8)


title: Sample 8: wt control 182 lumbar

tag: tissue

value: spinal cord (lumbar)

tag: sequencing batch

tag: age euthanized (days)

value: Wild Type


title: Sample 7: wt control 182 cervical

tag: genotype


title: Lin-Cd45-Cd71- Bone Marrow

source_name: Bone marrow

extract_protocol:
Fresh bone marrow cells were isolated by crushing mouse bones in media supplemented with FCS and the supernatant was collected. Cells were stained with fluorescently labelled antibodies against lineage markers (CD4, CD8, CD11b, B220, Gr1, Ter119), CD71 and CD45. A DNA dye was used to exclude debris. Single Lin-CD45-CD71-DNA+ cells were sorted into lysis buffer. Full-length cDNA from individual cells were produced following the Chromium Single Cell 3’ Reagent v2 protocol (10x genomics, Pleasanton, CA) according to manufacturer’s recommendations.
Default library production protocol, 10x genomics, Pleasanton, CA

value: Bone crushing, supernatant

value: No


title: Stage E7.0 endoderm single cell plate 1E2 cell (E7.0SCVE1-E2)

source_name: Mouse embryonic cells

tag: cell type


title: Stage E7.0 endoderm single cell plate 1D7 cell (E7.0SCVE1-D7)


title: S2P_fpa

tag: ecotype

value: anti-Ser2P (abcam ab5095, lot GR270578-1)


title: Lin-Cd45- Bone Marrow

extract_protocol:
Fresh bone marrow cells were isolated by crushing mouse bones in media supplemented with FCS and the supernatant was collected. Cells were stained with fluorescently labelled antibodies against lineage markers (CD4, CD8, CD11b, B220, Gr1, Ter119) and CD45. A DNA dye was used to exclude debris. Single CD45-DNA+ cells were sorted into PBS-2%FCS. Full-length cDNA from individual cells were produced following the Chromium Single Cell 3’ Reagent v2 protocol (10x genomics, Pleasanton, CA) according to manufacturer’s recommendations.
Default library production protocol, 10x genomics, Pleasanton, CA


title: Sample 6: wt control 220 lumbar

value: Batch 1


title: S2P_WT_rep1

value: 7-day old

value: NEBNext Ultra DNA library Prep kit (E7370)


title: Stage E7.0 endoderm single cell plate 1D6 cell (E7.0SCVE1-D6)

value: Mid-gastrulation embryo (E7.0)


title: Sample 5: wt control 220 cervical


title: Sample 4: wt control 181 lumbar


title: Total Bone Marrow

description: BM.total

extract_protocol:
Fresh bone marrow cells were isolated by crushing mouse bones in media supplemented with FCS and the supernatant was collected. Cells were stained with fluorescently labelled antibodies against lineage markers (CD4, CD8, CD11b, B220, Gr1, Ter119) and CD45. A DNA dye was used to exclude debris. Single DNA+ cells were sorted into PBS-2%FCS. Full-length cDNA from individual cells were produced following the Chromium Single Cell 3’ Reagent v2 protocol (10x genomics, Pleasanton, CA) according to manufacturer’s recommendations.
Default library production protocol, 10x genomics, Pleasanton, CA


title: Lin-Kit+ Bone Marrow

description: BM.Lin-Kit+

data_processing:
CellRanger 2.0.0, 10x genomics, Pleasanton, CA
Filtering of cells with less than 500 genes observed or more than 5% of molecules stemming from mitochondrial RNA. R-3.5.0, Seurat-2.3.3
R1 = barcode (basepairs 1-16) and UMI (basepairs 17-26)
R2 = biological read
Genome_build: mm10, cellranger version 1.2.0
Supplementary_files_format_and_content: Comma-separated value files of molecule (UMI) counts containing cells (post-filtering) in columns and genes in rows

extract_protocol:
Fresh bone marrow cells were isolated by crushing mouse bones in media supplemented with FCS and the supernatant was collected. Cells were stained with fluorescently labelled antibodies against lineage markers (CD4, CD8, CD11b, B220, Gr1, Ter119), and c-Kit. A DNA dye was used to exclude debris. Single Lin-Kit+DNA+ cells were sorted into PBS-2%FCS. Full-length cDNA from individual cells were produced following the Chromium Single Cell 3’ Reagent v2 protocol (10x genomics, Pleasanton, CA) according to manufacturer’s recommendations.
Default library production protocol, 10x genomics, Pleasanton, CA


title: RNAPII_bdrs_rep1

value: bdrs triple mutant

value: anti-RNAPII (abcam ab817, lot GR261055-2)


title: S2P_bdrs_rep1


title: Stage E7.0 endoderm single cell plate 1D5 cell (E7.0SCVE1-D5)


title: HIGH SINUSOIDS Sample S62

data_processing:
Alignment, STAR 2.6.0
Count tables, htseq-count 0.7.2
Filtering for 1 million reads per sample, R-3.5.0
Removal of outlier samples on PC 1 and 2, using PCA of variance stabilizing transformed counts, R-3.5.0, DESeq 1.20.0
Genome_build: Mus Musculus mm10, ENSEMBL release 38.73
Supplementary_files_format_and_content: Raw counts per gene, tab-separated values

source_name: Bone Marrow

extract_protocol:
Mouse femurs were fixed in 4% PFA and cryosectioned at 12 um thickness. Sections were stained using fluorescently labelled antibodies against Sca-1 and EMCN, and Hoechst 33342 was used as a counterstain. Samples were imaged and collected using the Zeiss PALM MicroBeam Axio Observer Z1 (Zeiss). Areas of 14500 µm2 on average, corresponding to around 250-300 cells, were isolated in proteinase K solution. Reverse crosslinked RNA was extracted with 100µl TRI Reagent (Sigma-Aldrich) following manufacturer instructions and cDNA synthesized following the SMARTER stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio, Japan) protocol.
SMARTER stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio, Japan)

value: bone marrow

tag: slide id

tag: area (micrometer2)

tag: niche

value: HIGH SINUSOIDS

tag: distance from endosteum

tag: filter

value: Insufficient Reads


title: Stage E7.0 endoderm single cell plate 1D4 cell (E7.0SCVE1-D4)

tag: developmental stage

tag: tag

value: Mouse embryonic cells


title: Sample 3: wt control 181 cervical

value: spinal cord (cervical)

tag: treatment


title: HIGH SINUSOIDS Sample S51

tag: strain


title: Stage E7.0 endoderm single cell plate 1D2 cell (E7.0SCVE1-D2)


title: RNAPII_fpa

value: fpa single mutant (fpa-7)

tag: age

tag: chip antibody

tag: library prep kit


title: RNAPII_WT_rep1

value: wild-type


title: ARTERIES Sample S61

tag: tissue

value: ARTERIES


title: Stage E7.0 endoderm single cell plate 1D3 cell (E7.0SCVE1-D3)


title: LOW SINUSOIDS Sample S9

value: LOW SINUSOIDS

value: OK